A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

abortTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Request that the ObjectStore aborts and closes the transaction, delegate to internal ObjectStoreWriter.

abortTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Request that the ObjectStoreWriter aborts and closes the transaction

abortTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Request that the ObjectStoreWriter aborts and closes the transaction

abortTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Aborts a transaction.

AbstractConstraint - Class in org.intermine.sql.query

An abstract representation of an item that can be present in the WHERE or HAVING sections of an SQL query.

AbstractConstraint() - Constructor for class org.intermine.sql.query.AbstractConstraint

AbstractHelper - Class in org.intermine.api.query.range

A class that can be extended to easily create RangeHelpers for a particular type.

AbstractHelper() - Constructor for class org.intermine.api.query.range.AbstractHelper

AbstractListService - Class in org.intermine.webservice.server.lists

Base class for list services.

AbstractListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AbstractListService

AbstractQueryService<T> - Class in org.intermine.webservice.client.services

Common behaviour for services requesting results from a web-service.

AbstractQueryService(String, String, String) - Constructor for class org.intermine.webservice.client.services.AbstractQueryService

Constructor.

AbstractQueryService - Class in org.intermine.webservice.server.query

A base class for query services.

AbstractQueryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.AbstractQueryService

Constructor.

AbstractTable - Class in org.intermine.sql.query

An abstract representation of an item that can be present in the FROM section of an SQL query.

AbstractTable() - Constructor for class org.intermine.sql.query.AbstractTable

AbstractTracker - Class in org.intermine.api.tracker

Abstract interface for creating trackers objects.

AbstractTracker(Queue<Track>, String) - Constructor for class org.intermine.api.tracker.AbstractTracker

Construct a Tracker setting the tracks queue and the table name

AbstractValue - Class in org.intermine.sql.query

An abstract representation of an item that can be present in the SELECT, GROUP BY, or ORDER BY sections of an SQL query, as well as in a constraint.

AbstractValue() - Constructor for class org.intermine.sql.query.AbstractValue

accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either

How you go about accessing the values.

accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Left

accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Right

AcceptanceTestTask - Class in org.intermine.task

A Task to run acceptance tests, configurable from a file.

AcceptanceTestTask() - Constructor for class org.intermine.task.AcceptanceTestTask

acceptInvitation(SharingInvite, Profile) - Method in class org.intermine.api.bag.SharedBagManager

Accept this invitation.

act(Emailer) - Method in interface org.intermine.web.context.MailAction

Inject an emailer, and do something.

action - Variable in class org.intermine.api.search.TaggingEvent

ADD - Static variable in class org.intermine.objectstore.query.QueryExpression

Addition of two numeric fields

add(Query) - Method in class org.intermine.sql.precompute.BestQuery

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.BestQuery

Allows a Query to be added to this tracker.

add(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Allows a Query to be added to this tracker.

add(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Allows a Candidate to be added to this tracker.

add(Query) - Method in class org.intermine.sql.precompute.BestQueryFallback

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.BestQueryFallback

Allows a Query to be added to this tracker.

add(Query) - Method in class org.intermine.sql.precompute.BestQueryLogger

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.BestQueryLogger

Allows a Query to be added to this tracker.

add(Query) - Method in class org.intermine.sql.precompute.BestQueryStorer

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.BestQueryStorer

Allows a Query to be added to this tracker.

add(Query) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery

Allows a Query to be added to this tracker.

add(String) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery

Allows a Query to be added to this tracker.

add(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Add a precomputed table to the underlying database.

add(PrecomputedTable, Collection<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Add a precomputed table to the underlying database.

add(AbstractConstraint) - Method in class org.intermine.sql.query.ConstraintSet

Add an AbstractConstraint to this ConstraintSet.

add(AbstractValue) - Method in class org.intermine.sql.query.Function

Adds an operand to this Function object.

add(Constant) - Method in class org.intermine.sql.query.InListConstraint

Add constants to the list.

add(E) - Method in class org.intermine.util.ConsistentSet

Add an object to the set.

add(Integer) - Method in class org.intermine.util.IntPresentSet

Adds an int to the set.

add(E) - Method in class org.intermine.util.PseudoSet

add(Object) - Method in class org.intermine.web.logic.results.InlineResultsTableRow

Add an InlineTableResultElement or an empty String

add(Item) - Method in class org.intermine.webservice.client.lists.ItemList

add(Object) - Method in class org.intermine.webservice.client.results.ResultRowList

add(int, Object) - Method in class org.intermine.webservice.client.results.ResultRowList

ADD_HEADER_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

The parameter for requesting column headers

addAccession(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addAll(Collection<? extends Constant>) - Method in class org.intermine.sql.query.InListConstraint

Adds a Collection of Constants to the list.

addAll(Collection<? extends E>) - Method in class org.intermine.util.ConsistentSet

Add a whole Collection of objects to the set.

addAll(Collection<? extends E>) - Method in class org.intermine.util.PseudoSet

addAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList

addAll(Collection<? extends Object>) - Method in class org.intermine.webservice.client.results.ResultRowList

addAll(int, Collection<? extends Object>) - Method in class org.intermine.webservice.client.results.ResultRowList

addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Adds a collection of elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.

addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Adds a collection of elements to an ObjectStoreBag.

addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Adds a collection of elements to an ObjectStoreBag.

addAllToBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Adds elements to the given bag.

addAnchor(String) - Method in class org.intermine.web.struts.ForwardParameters

Add an anchor to the path.

addAndConstraint(Query, Constraint) - Static method in class org.intermine.objectstore.query.QueryHelper

Add a constraint to be ANDed with those present in a Query.

addAspectSource(AspectSource) - Method in class org.intermine.web.logic.aspects.Aspect

Add a AspectSource.

addAttribute(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

holds the value until the item is processed/stored on the next line

addAttribute(Attribute) - Method in class org.intermine.xml.full.Item

Add an attribute.

addBag(ObjectStoreBag) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

Adds a bag to this combination

addBagCombination(ObjectStoreBagCombination) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

addBagDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type

Add a bag displayer for this Type

addBagValues() - Method in class org.intermine.api.profile.InterMineBag

Save the key field values associated to the bag into bagvalues table

addBagValues(Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag

Save the values given in input into bagvalues table

addBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

addByChadoId(Integer, ChadoCVTerm) - Method in class org.intermine.bio.chado.ChadoCV

Add a cvterm and its chado id to this cv.

addCacheLine(String, String, int) - Method in class org.intermine.sql.precompute.OptimiserCache

Adds a new OptimiserCacheLine object to the cache.

addCanonicalIsoform(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

sets isIsoform to be false.

addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.And

Adds a node to the collection of children.

addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Operator

Adds a node to the collection of children.

addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Or

Adds a node to the collection of children.

addClass(LuceneObjectClass) - Method in class org.intermine.web.autocompletion.LuceneIndex

added a new LuceneObjectClass to internal map

addCollection(ReferenceList) - Method in class org.intermine.xml.full.Item

Add a collection.

addCollectionToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Adds a new list, representing a collection to the current node (map)

addColumn(Database, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil

Add a column in the table specified in input.

addColumn(Connection, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil

Add a column to an existing database table, if it does not already exist.

AddColumnAction - Class in org.intermine.web.struts

AddColumnAction adds new column to existing WebTable that should be displayed.

AddColumnAction() - Constructor for class org.intermine.web.struts.AddColumnAction

addColumns(List<Path>) - Method in class org.intermine.api.results.WebResults

addColumns(List<Path>) - Method in interface org.intermine.api.results.WebTable

Adds columns that should be displayed to the table.

addCommentRefId(String, Integer) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addComponent(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet

Add a Constraint to the set

addConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery

Adds a PathConstraint to this query.

addConstraint(PathConstraint, String) - Method in class org.intermine.pathquery.PathQuery

Adds a PathConstraints to this query, associated with a given constraint code.

addConstraints(Collection<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery

Adds a collection of constraints to this query.

addConstraints(PathConstraint...) - Method in class org.intermine.pathquery.PathQuery

Adds a group of constraints to this query.

addCVTermColon(String) - Static method in class org.intermine.bio.dataconversion.FlyBaseProcessor

For a FlyBase cvterm identifier like "FBbt00000001", add a colon in the middle and return: "FBbt:00000001"

addDataSet(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Add an DataSet Item to this handler, to be retrieved later with getDataSetReferenceList().

addDbref(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

add dbref to list.

addEarlyItem(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Add a new Item to the Collection returned by getItems, at the beginning.

addECNumber(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addElement(StringBuilder, String, String) - Method in class org.intermine.webservice.server.output.XMLFormatter

Add an element with some content.

addEntry(String, String, String, Collection<String>, Boolean) - Method in class org.intermine.bio.dataconversion.IdResolver

Add an entry to the IdResolver, a primary identifier and any number of synonyms.

addEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry.Comment

Will be replaced later with publication

addExecution(TemplateTrack) - Method in class org.intermine.api.tracker.TemplatesExecutionMap

Add a new template track into the map

addFeature(Item) - Method in class org.intermine.bio.dataconversion.UniprotEntry

new feature for protein feature.type and feature.description are set first.

addFeatureLocation(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

addField added field to the class

addFieldConfig(FieldConfig) - Method in class org.intermine.web.logic.config.Type

Add a FieldConfig for this Type

addFieldToMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Adds the attributes contained in the cell to the map given.

addFileSet(FileSet) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask

Set the source fileset.

addFileSet(FileSet) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the data fileset

addFileSet(FileSet) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set the data fileset

addFileSet(FileSet) - Method in class org.intermine.task.FileConverterTask

Set the data fileset

addFileSet(FileSet) - Method in class org.intermine.task.FileDirectDataLoaderTask

Add a FileSet to read from.

addFileSet(FileSet) - Method in class org.intermine.task.FullXmlConverterTask

Set the data fileset

addFrom(FromElement) - Method in interface org.intermine.objectstore.query.HasFromList

Adds a FromElement to the FROM clause of this Query

addFrom(FromElement) - Method in class org.intermine.objectstore.query.Query

Adds a FromElement to the FROM clause of this Query

addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.Query

Adds a FromElement to the FROM clause of this Query

addFrom(FromElement) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Adds an element to the FROM list.

addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Adds an element to the FROM list, including an alias.

addFrom(AbstractTable) - Method in class org.intermine.sql.query.Query

Adds a table to the from list of this query.

addGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

geneDesignation is required in the case of a single protein having multiple gene identifiers.

addGeneName(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

From

addGlobalRepository() - Method in class org.intermine.api.search.SearchRepository

Add a global repository

addGOEvidence(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addGOTerm(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addGroupBy(AbstractValue) - Method in class org.intermine.sql.query.Query

Adds a field to the GROUP BY clause of this query.

addHaving(AbstractConstraint) - Method in class org.intermine.sql.query.Query

Adds a constraint to the HAVING clause of this query.

addHeaderConfigLink(HeaderConfigLink) - Method in class org.intermine.web.logic.config.Type

Add a header configuration, used from WebConfig

addHeaderConfigTitle(HeaderConfigTitle) - Method in class org.intermine.web.logic.config.Type

Add a header configuration, used from WebConfig

addIdentifier(String, String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

example: 6239.primaryIdentifier.dbref = WormBase 6239.secondaryIdentifier.name = ORF [taxonId].

addIdsFromResultSet(ResultSet, OrganismRepository, String) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Add results from query to ID resolver

addIdsFromResultSet(ResultSet) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

Add results from query to ID resolver

addIdsToBag(Collection<Integer>, String) - Method in class org.intermine.api.profile.InterMineBag

Add the given ids to the bag, this updates the bag contents in the database.

addIdsToList(Collection<? extends String>, InterMineBag, String, String, Set<String>, Collection<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService

Adds objects to the a bag for the matches against a set of identifiers.

addIdToBag(Integer, String) - Method in class org.intermine.api.profile.InterMineBag

Add the given id to the bag, this updates the bag contents in the database. he type can be a qualified or un-qualified class name.

addIndex(String, String, Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Adds an index to the given table on the given field.

addInlineList(InlineListConfig) - Method in class org.intermine.web.logic.config.Type

Add an InlineList for this object, used from WebConfig

addIsoform(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addIsoformSynonym(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

if an isoform has two ID tags, then the first one is used and the second one is added as a synonym

addIssue(String, String, String, List) - Method in class org.intermine.api.bag.BagQueryResult

Add an issue to this result.

addItem(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Add a new Item to the Collection returned by getItems().

AdditionalConverter - Class in org.intermine.api.bag

Represents an additional converter config

AdditionalConverter(String, String, String, String, String) - Constructor for class org.intermine.api.bag.AdditionalConverter

Create a new AdditionalConverter object.

additionsFiles - Variable in class org.intermine.task.ModelMergerTask

addJsonProperty(StringBuffer, String, Object) - Method in class org.intermine.pathquery.PathQuery

Add a JSON property when serialising

addKey(Map<String, List<FieldDescriptor>>, String, FieldDescriptor) - Static method in class org.intermine.api.config.ClassKeyHelper

Add a key to set of keys for a given class.

addKeyword(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addLongDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type

Add a long displayer for this Type

addMainIds(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Add alternative main identifiers for a primary identifier to the IdResolver.

addMainIds(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Add alternative main identifiers for a primary identifier to the IdResolver.

addMatch(String, Integer) - Method in class org.intermine.api.bag.BagQueryResult

Add a new match from an input string to an InterMineObject id.

addModel(Model) - Method in class org.intermine.pathquery.PathQueryHandler

addNonCoveredFrom(Set<T>, Set<T>, Set<T>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Adds all required FROM items to the FROM list of the new query.

addObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag

addObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable

Add this observer to the list of interested parties.

addObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate

addOrderBy(String, OrderDirection) - Method in class org.intermine.pathquery.PathQuery

Adds an element to the order by list of this query.

addOrderBy(OrderElement) - Method in class org.intermine.pathquery.PathQuery

Adds an element to the order by list of this query.

addOrderBy(AbstractValue) - Method in class org.intermine.sql.query.Query

Adds a field to the ORDER BY clause of this query.

addOrderBys(Collection<OrderElement>) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the order by list of this query.

addOrderBys(OrderElement...) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the order by list of this query.

addOrderBySpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the order by list, given a space-separated list.

addOutputAttribute(String, String) - Method in class org.intermine.webservice.server.widget.WidgetService

Wrapper around addOutputInfo that makes sure we don't add empty values.

addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.GraphService

addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.TableWidgetService

addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetService

Add metadata about the widget we are using.

addOutputFilter(WidgetConfig, String, InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService

Add information about the filters as attributes to the result.

addOutputInfo(String, String) - Method in class org.intermine.webservice.server.core.JSONService

Add a key value pair to put in the header of json results.

addOutputListInfo(InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService

Add metadata about the list we are processing.

addOutputResult(Widget) - Method in class org.intermine.webservice.server.widget.WidgetService

Send results to the outside world.

addParam(String, String) - Method in class org.intermine.web.logic.config.Displayer

Add a stored parameter to this Displayer.

addParameter(String, String) - Method in class org.intermine.web.struts.ForwardParameters

Add a parameter to the path.

addParameter(String, String) - Method in interface org.intermine.webservice.client.core.Request

Adds parameter.

addParameter(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl

Adds parameter.

addParent(String) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

addProteinName(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

the name section in uniprot can contain several names, eg. recommendedName, alternateName, etc.

addPub(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addPubEvidence(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

addPublication(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Add an Publication Item to this handler, to be retrieved later with getPublicationReferenceList().

addRange(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

addReference(Query, QueryClass, String, String) - Method in class org.intermine.web.logic.widget.WidgetLdr

Add a contains constraint to Query (q) built with the query class and attribute given in input

addReference(Reference) - Method in class org.intermine.xml.full.Item

Add a reference.

addReferenceConstraint(Model, Query, QueryClass, String, QueryClass, boolean) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Add a contains constraint to Query (q) from qcStart from qcEnd via reference refName.

addReferencedCellToJsonMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Adds the information from a cell representing a reference to the map given.

addReferenceToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Adds an intermediate reference to the current node.

addRefId(String) - Method in class org.intermine.xml.full.ReferenceList

Add a value to the list of references.

addReportDisplayer(ReportDisplayerConfig) - Method in class org.intermine.web.logic.config.WebConfig

Add config for a report page displayer.

addRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager

Adds a request to the Set of pending requests, and wakes up a Thread to handle it.

addResolverEntry(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Create entries for the IdResolver, these will be added when getIdResolver is called.

addResolverEntry(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Create entries for the IdResolver, these will be added when getIdResolver is called.

addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable

Add a result element (RE or "" String)

addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable

Add a result element (RE or "" String), used for type safety as overriden on BagUploadConfirm

addResultEntries(Collection<Map.Entry<String, Object>>) - Method in class org.intermine.webservice.server.core.JSONService

addResultEntries(Collection<Map.Entry<String, Object>>, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a bunch of entries.

addResultEntry(String, Object, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a single entry.

addResultEntry(Map.Entry<String, Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a single entry.

addResultItem(Map<String, ? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a map of names and values as a JSON object.

addResultItem(List<? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a list of objects as a JSON array.

addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.MemoryOutput

Add result item to memory.

addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.Output

Adds data to output.

addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.StreamedOutput

Forwards data to associated writer

addResultValue(CharSequence, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a char-sequence as a JSON value.

addResultValue(Number, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a number as a JSON value.

addResultValue(Boolean, boolean) - Method in class org.intermine.webservice.server.core.JSONService

Output a bool as a JSON value.

addRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

Add a role to this permission.

addRow(Connection, String, Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.Batch

Adds a row to the batch for a given table.

addRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch

Adds a row to the batch for a given indirection table.

addRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Adds a row to the batch.

addRow(Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.TableBatch

Adds a row to the batch.

addSelect(SelectValue) - Method in class org.intermine.sql.query.Query

Adds a field to the select list of this query.

addSelectedToBag(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Adds the selected object ids to the given bag.

addSubtab(String, String) - Method in class org.intermine.web.logic.results.WebState

Set the subtab for a particular tab

addSummaryConstraint(SummaryConstraint) - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Add a constraint to that applies to this path.

addSynonym(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Keep track of the synonyms per line.

addSynonym(OboTermSynonym) - Method in class org.intermine.bio.ontology.OboTerm

Add a synonym for this term.

addSynonyms(List<String>) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Keep track of the synonyms per line.

addSynonyms(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Add synonyms for a primary identifier to the IdResolver

addSynonyms(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Add synonyms for a primary identifier to the IdResolver

addSynonyms(OboTerm, List<?>, String) - Method in class org.intermine.bio.ontology.OboParser

Add synonyms to a DagTerm.

addTableExportConfig(TableExportConfig) - Method in class org.intermine.web.logic.config.WebConfig

Add an TableExportConfig to the Map of TableExportConfig objects using tableExportConfig.getId() as the Map key.

addTableToDatabase(PrecomputedTable, Collection<String>, boolean) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Add a PrecomputedTable to the database.

addTag(String, String, String, Profile) - Method in class org.intermine.api.profile.TagManager

Add a new tag.

addTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager

Associate a websearchable obj with a certain tag.

addTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager

Associate a class with a certain tag.

addTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager

Associate a reference with a certain tag.

addTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices

Adds tag and assures that there is only one tag for this combination of tag name, tagged Object and type.

addTag(String) - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo

Add a tag to the set of tags to apply.

addTags(String...) - Method in class org.intermine.webservice.client.lists.ItemList

Add some new tags to this list.

addTags(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService

Get the tags for a list after adding some to the tag set.

addTags(Collection<? extends String>) - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo

Add some tags to the set of tags to apply.

addTagsToBag(Collection<String>, InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager

Add tags to a bag.

addTime(long) - Method in class org.intermine.objectstore.intermine.ExtraQueryTime

Adds statistics for an executed query to this object.

addTitleParts(HashMap<String, List<HeaderConfigTitle.TitlePart>>) - Method in class org.intermine.web.logic.config.HeaderConfigTitle

Add title parts to this header config.

addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Adds an element to an ObjectStoreBag, delegate to internal ObjectStoreWriter.

addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Adds an element to an ObjectStoreBag.

addToBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Adds an element to an ObjectStoreBag.

AddToBagAction - Class in org.intermine.web.struts

Action to save a single object o an existing bag.

AddToBagAction() - Constructor for class org.intermine.web.struts.AddToBagAction

addToBagFromQuery(Query) - Method in class org.intermine.api.profile.InterMineBag

Add elements to the bag from a query, this is able to operate entirely in the database without needing to read objects into memory.

addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Adds elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.

addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Adds elements to an ObjectStoreBag from the results of a Query.

addToBagFromQuery(ObjectStoreBag, Query) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Adds elements to an ObjectStoreBag from the results of a Query.

addToBagFromQueryWithConnection(Connection, ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Adds elements to a bag from the results of a query.

addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Add an object to another object's collection, delegate to internal ObjectStoreWriter.

addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Place an object in a many-to-many collection of another object.

addToCollection(Integer, Class<?>, String, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Place an object in a many-to-many collection of another object.

addToCollection(String, Item) - Method in class org.intermine.xml.full.Item

Add the identifier of the given Item to a collection.

addToCollection(String, String) - Method in class org.intermine.xml.full.Item

Add a reference to a collection of this item.

addToCollectionWithConnection(Connection, Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Performs addToCollection with given connection

addToConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper

Add a constraint code to a logic expression, ANDed with any constraints already in the expression, e.g.

addToFeatureMap(Integer, FeatureData) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Override method that adds completed features to featureMap.

addToFeatureMap(Integer, FeatureData) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Add feature data to FeatureMap, can be overidden by subclasses that need to store some features in additional maps.

addToFrom(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

addToGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query

Add a QueryNode to the GROUP BY clause of this Query

addToHolder(Object) - Method in class org.intermine.util.CacheHoldingArrayList

Adds an object to the holder.

addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl

Adds a statement to the lastBatch.

addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Adds a statement to the lastBatch.

addToList(List<Constraint>, Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Adds all the constraints present in the argument into the given List.

addToOrderBy(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

addToOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query

Add a QueryOrderable to the ORDER BY clause of this Query

addToOrderBy(QueryOrderable, String) - Method in class org.intermine.objectstore.query.Query

Add a QueryOrderable to the ORDER BY clause of this Query

addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl

Adds a statement to the postDeleteBatch.

addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Adds a statement to the postDeleteBatch.

addToPreDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Adds a statement to the preDeleteBatch.

addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query

Add a QuerySelectable to the SELECT clause of this Query

addToSelect(QuerySelectable, String) - Method in class org.intermine.objectstore.query.Query

Add a QuerySelectable to the SELECT clause of this Query

addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.Queryable

Adds an element to the SELECT list.

addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Adds an element to the SELECT list.

addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Adds an element to the SELECT list.

addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect

Adds an element to the SELECT list.

addToSortOrder(String, String) - Method in class org.intermine.dwr.AjaxServices

Add a Node from the sort order

addToUnion(Query) - Method in class org.intermine.sql.query.Query

Adds another Query to the UNION set of this query.

addToView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Add a path to the results view.

addToWhere(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

addType(Type) - Method in class org.intermine.web.logic.config.WebConfig

Add a type to the WebConfig Map.

addUniqueItemId(String, String) - Method in class org.intermine.dataconversion.DataConverter

List of unique identifiers and their refIds.

addUnmatchedId(String) - Method in class org.intermine.webservice.client.lists.ItemList

Add a new unmatched id to the set of unmatched identifiers.

addUnmatchedIds(Collection<String>) - Method in class org.intermine.webservice.client.lists.ItemList

Add some new unmatched ids to the set of unmatched identifiers.

addUnresolved(Collection<String>) - Method in class org.intermine.api.bag.BagQueryResult

Set the Map of unresolved input strings.

addUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices

Share the bag given in input with the user which userName is input and send email

addValueToField(String, String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

addValueToField added a new value to one existing field

addView(String) - Method in class org.intermine.pathquery.PathQuery

Add a single element to the view list.

addViews(Collection<String>) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the view list.

addViews(String...) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the view list.

addViewSpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery

Adds a group of elements to the view list, given a space-separated list.

addWhere(AbstractConstraint) - Method in class org.intermine.sql.query.Query

Adds a constraint to the where clause for this query.

addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.Type

Add a widget to the Type

addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.WebConfig

addXref(OboTerm) - Method in class org.intermine.bio.ontology.OboTerm

Add a xref for this term.

addXrefs(OboTerm, List<?>) - Method in class org.intermine.bio.ontology.OboParser

Add xrefs to a DagTerm.

aDescendsFromB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Test whether a class named "a" descends from a class named "b".

adjustPValues(ErrorCorrection.Strategy, Map<String, BigDecimal>, Double, int) - Static method in class org.intermine.web.logic.widget.ErrorCorrection

advance(int) - Method in class org.intermine.webservice.client.results.Page

Advance to a new page my a given number of steps.

af - Variable in class org.intermine.web.struts.ForwardParameters

Original ActionForward.

aIsaB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Test whether a class named "A" is, or descends from, a class named "B".

ajaxCollapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - collapse a model browser node.

ajaxEditConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - edit an existing constraint.

ajaxEditJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Edit a constraint's join style settings for a path, and forward to queryBuilderConstraint, for use by ajax.

ajaxEditTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - edit a template constraint.

ajaxExpand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - expand a model browser node.

ajaxNewConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - ahow the panel for adding a new constraint to the query.

ajaxRenderPaths(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

AJAX request - render query paths.

AjaxServices - Class in org.intermine.dwr

This class contains the methods called through DWR Ajax

AjaxServices() - Constructor for class org.intermine.dwr.AjaxServices

ajaxShowDisplayer(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

Show a displayer in response to an AJAX request.

ajaxTemplateCount(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

Count number of results for a template for inline templates

ajaxVerbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

AKA - Static variable in class org.intermine.api.profile.UserPreferences

What we should call the user.

ALIAS - Static variable in class org.intermine.api.profile.UserPreferences

The alias of this user.

alias(String) - Method in class org.intermine.dataconversion.DataConverter

Uniquely alias a className

alias(Object, String) - Method in class org.intermine.objectstore.query.Query

Set an alias for an element in the Query.

alias - Variable in class org.intermine.sql.query.AbstractTable

alias - Variable in class org.intermine.sql.query.SelectValue

alias - Variable in class org.intermine.task.DropPrecomputedTablesTask

alias - Variable in class org.intermine.task.PrecomputeTask

alias - Variable in class org.intermine.task.RunIqlQueryTask

alias - Variable in class org.intermine.task.SummariseObjectStoreTask

alias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

ALL - Static variable in class org.intermine.api.search.Scope

User or global scope for bags, templates, etc.

ALL_BAGS - Static variable in class org.intermine.api.search.SearchTarget

The search target for all bags

ALL_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint

ALL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget

The search target for all templates

ALLBUTINTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination

Constant representing an all but intersect operation

allPkClassesEmptyForClass - Variable in class org.intermine.dataloader.HintingFetcher

allSources - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

ALT_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput

The name of the new list (synonym)

alterComparisonAnd(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take a couple of integers as if they are values returned by compare, and assume that they are two loose (and possibly different) descriptions of the relation between the same two AbstractConstraints, and return a value that is a more strict description.

alterComparisonAORB(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take a couple of integers as if they are values returned by compare, for this compared to A, and this compared to B, and return the value that compare should return for this compared to (A OR B).

alterComparisonNotObj(int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take an integer as if it is a value returned by compare, and return the value that compare would have returned if second constraint (obj) had been NOTed.

alterComparisonNotThis(int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take an integer as if it is a value returned by compare, and return the value that compare would have returned if first constraint (this) had been NOTed.

alterComparisonSwitch(int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take an integer as if it is a value returned by compare, and return the value that compare would have returned if this and obj had been switched.

ALWAYS_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer

AlwaysMap<K,V> - Class in org.intermine.util

This is a dumb implementation of a Map.

AlwaysMap(V) - Constructor for class org.intermine.util.AlwaysMap

Construct an AlwaysMap.

AlwaysSet<E> - Class in org.intermine.util

A Set that always returns true for the contains method.

amendTo(String) - Method in class org.intermine.api.profile.InvalidBag

Fix this bag by changing its type.

analyse(Database, boolean) - Static method in class org.intermine.sql.DatabaseUtil

Analyse given database, perform vacuum full analyse if full parameter true.

analyse(Database, ClassDescriptor, boolean) - Static method in class org.intermine.sql.DatabaseUtil

Analyse database table for a given class and all associated indirection tables.

AnalyseDbTask - Class in org.intermine.task

Task to run ANALYSE on a table or whole database.

AnalyseDbTask() - Constructor for class org.intermine.task.AnalyseDbTask

anchor - Variable in class org.intermine.web.struts.ForwardParameters

Anchor name.

and(EitherVisitor<A, B, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor

Compose this visitor with another visitor which handles the either after this one has had a go at it, presumably for side-effects like logging and what-not.

annotationClassName - Variable in class org.intermine.bio.dataconversion.GoConverter

AnonProfile - Class in org.intermine.api.util

A null-object for profiles for use with the web services.

AnonProfile() - Constructor for class org.intermine.api.util.AnonProfile

Constructor

API - Interface in org.intermine.api

The interface of the API, abstracted for testing purposes.

api - Variable in class org.intermine.webservice.server.core.WebServiceServlet

ApiJavaController - Class in org.intermine.web.struts

ApiJavaController() - Constructor for class org.intermine.web.struts.ApiJavaController

ApiPerlController - Class in org.intermine.web.struts

ApiPerlController() - Constructor for class org.intermine.web.struts.ApiPerlController

ApiTemplate - Class in org.intermine.api.template

This class extends TemplateQuery to provide the features needed by the API - Lucene indexing and database serialisation.

ApiTemplate(String, String, String, PathQuery) - Constructor for class org.intermine.api.template.ApiTemplate

ApiTemplate(TemplateQuery) - Constructor for class org.intermine.api.template.ApiTemplate

Construct a new API template that has all the same properties as the TemplateQuery passed into the constructor.

apiTemplateMapToJson(InterMineAPI, Map<String, ApiTemplate>) - Static method in class org.intermine.api.template.TemplateHelper

Helper routine for serialising a map of templates to JSON.

apiTemplateMapToXml(Map<String, ApiTemplate>, int) - Static method in class org.intermine.api.template.TemplateHelper

Serialse a map of templates to XML.

append(String) - Method in class org.intermine.pathquery.Path

Return new Path that has this Path as its prefix and has fieldName as the last element.

append(String...) - Method in class org.intermine.webservice.client.lists.ItemList

Add new items to the list by resolving the identifiers of objects.

append(Collection<? extends String>) - Method in class org.intermine.webservice.client.lists.ItemList

Add new items to the list by resolving the identifiers of objects.

append(Item...) - Method in class org.intermine.webservice.client.lists.ItemList

Add new items to the list.

append(PathQuery) - Method in class org.intermine.webservice.client.lists.ItemList

Add new items to the list by resolving the identifiers of objects.

append(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService

Append some objects corresponding to identifiers to the given list, returning a list representing the new state.

append(ItemList, Collection<? extends String>) - Method in class org.intermine.webservice.client.services.ListService

Append some objects corresponding to identifiers to the given list, returning a list representing the new state.

append(ItemList, PathQuery) - Method in class org.intermine.webservice.client.services.ListService

Append the objects contained in the result set of a given query to the given list, returning a list representing the new state.

APPLICATION_JSON - Static variable in class org.intermine.webservice.client.core.ContentType

A ContentType constant that describes the JSON content type.

APPLICATION_JSON_OBJ - Static variable in class org.intermine.webservice.client.core.ContentType

A Content type that describes the JSON objects content type.

APPLICATION_JSON_ROW - Static variable in class org.intermine.webservice.client.core.ContentType

A Content type that describes the JSON rows content type.

apply(Constraint) - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint

Perform test for NOT NULL constraint on node

apply(Constraint) - Method in interface org.intermine.objectstore.query.ConstraintTraverseAction

The apply() method is called by ConstraintHelper.traverseConstraints() for each Constraint and sub-Constraint.

apply(Map<String, BigDecimal>, PopulationInfo, Map<String, PopulationInfo>, Double) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Apply the correction coefficient to the pValuesTerm given in input

asList() - Method in class org.intermine.api.search.SearchResult

A list of between two and three items containing the information in this result.

asList() - Method in interface org.intermine.objectstore.proxy.LazyCollection

Return this Collection as a List.

asList() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Return this Collection as a List.

asList() - Method in class org.intermine.objectstore.query.Results

Return this Collection as a List.

Aspect - Class in org.intermine.web.logic.aspects

Configuration for a single data set.

Aspect() - Constructor for class org.intermine.web.logic.aspects.Aspect

AspectBinding - Class in org.intermine.web.logic.aspects

Routines for unmarshaling Aspect objects from XML.

AspectController - Class in org.intermine.web.struts

Contoller for a single data set tile embedded in a page.

AspectController() - Constructor for class org.intermine.web.struts.AspectController

ASPECTS - Static variable in class org.intermine.web.logic.Constants

Servlet context attribute - map from aspect set name to Aspect object.

AspectSource - Class in org.intermine.web.logic.aspects

Describes a source of data contributing to some data set.

AspectSource() - Constructor for class org.intermine.web.logic.aspects.AspectSource

AspectTagUtil - Class in org.intermine.api.tag

Util class for working with aspect tags.

assignMapping(Integer, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Puts a mapping into idMap.

assureOutputFormatSpecified(Request) - Method in class org.intermine.webservice.client.core.Service

Add a format parameter to match the content-type if there is one.

assureSize(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream

Resizes the buffer to ensure it is as large as newSize.

ASYMMETRIC_SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations

Constant representing logical asymmetric substraction.

AsymmetricOperationInput - Class in org.intermine.webservice.server.lists

A list input class for operations that have a left and a right side.

AsymmetricOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.AsymmetricOperationInput

Constructor.

asymmetricSubtract(Model, Collection<InterMineBag>, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations

AT_LEAST - Static variable in class org.intermine.objectstore.query.ResultsInfo

Denotes that the known number of rows has a minimum which exceed the estimate.

AT_MOST - Static variable in class org.intermine.objectstore.query.ResultsInfo

Denotes that the known number of rows has a maximum, and the estimate exceeds it.

ATTR_MARKER_RE - Static variable in class org.intermine.api.LinkRedirectManager

Attribute - Class in org.intermine.xml.full

Representation of an Attribute in an object

Attribute() - Constructor for class org.intermine.xml.full.Attribute

Constructor

Attribute(String, String) - Constructor for class org.intermine.xml.full.Attribute

Construnctor

ATTRIBUTE_TYPES - Static variable in class org.intermine.pathquery.PathQueryHandler

This is a list of String type descriptions that are attribute types

AttributeLinkURL - Class in org.intermine.web.util

Simple class that parses provided url.

AttributeLinkURL(String) - Constructor for class org.intermine.web.util.AttributeLinkURL

Constructor.

attributeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

attributeOptions - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

attributes - Variable in class org.intermine.webservice.server.query.result.QueryResultService

attributeValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

AuthenticatedListService - Class in org.intermine.webservice.server.lists

A Class that insists on being authenticated.

AuthenticatedListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AuthenticatedListService

Constructor.

Authenticator - Class in org.intermine.web.struts.oauth2

The action that bounces the user off to their respective authentication provider when they want to use them to log-in with OAuth2.

Authenticator() - Constructor for class org.intermine.web.struts.oauth2.Authenticator

AUTO_COMPLETER - Static variable in class org.intermine.web.logic.Constants

ServletContext attribute, autocompletion.

AUTOCOMPLETE_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key to use to store the autocomplete RAMIndexes.

AutoCompleter - Class in org.intermine.web.autocompletion

Autocompleter class for initializing and using the autocompletion

AutoCompleter() - Constructor for class org.intermine.web.autocompletion.AutoCompleter

Autocompleter standard constructor.

AutoCompleter(ObjectStore, Properties) - Constructor for class org.intermine.web.autocompletion.AutoCompleter

Autocompleter build index constructor.

AutoCompleter(InputStream) - Constructor for class org.intermine.web.autocompletion.AutoCompleter

Autocompleter rebuild constructor.

AvailableColumnsController - Class in org.intermine.web.struts

Controller for availableColumns.tile.

AvailableColumnsController() - Constructor for class org.intermine.web.struts.AvailableColumnsController

AvailableListsService - Class in org.intermine.webservice.server.lists

A service to report what lists a user has access to, and some details of those lists.

AvailableListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AvailableListsService

Constructor

AvailableListsServlet - Class in org.intermine.webservice.server.lists

AvailableListsServlet() - Constructor for class org.intermine.webservice.server.lists.AvailableListsServlet

AvailableServicesServlet - Class in org.intermine.webservice.server

Report whether a requested service is implementented on this mine.

AvailableServicesServlet() - Constructor for class org.intermine.webservice.server.AvailableServicesServlet

AvailableTemplatesService - Class in org.intermine.webservice.server.template

Fetch the names of public template queries for use with the Templates web service.

AvailableTemplatesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.AvailableTemplatesService

Constructor.

AvailableWidgetsService - Class in org.intermine.webservice.server.widget

A service for listing the available widgets.

AvailableWidgetsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsService

Constructor

AvailableWidgetsServlet - Class in org.intermine.webservice.server.widget

Servlet handling requests for information about which widgets are available.

AvailableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsServlet

AVERAGE - Static variable in class org.intermine.objectstore.query.QueryFunction

Average value of a number of rows

AVG - Static variable in class org.intermine.sql.query.Function

AVG(v) aggregate function - takes one operand.

B

backgroundFlush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch

Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.

backgroundFlush(Connection, Set<String>, boolean) - Method in class org.intermine.sql.writebatch.Batch

Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.

BadQueryException - Exception in org.intermine.api.query

BadQueryException(String, Exception) - Constructor for exception org.intermine.api.query.BadQueryException

BadRequestException - Exception in org.intermine.webservice.client.exceptions

The BadRequestException is thrown by service when there is a problem with the request.

BadRequestException(String) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException

BadRequestException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException

BadRequestException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException

BadRequestException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException

BadRequestException - Exception in org.intermine.webservice.server.exceptions

The BadRequestException is thrown by service when there is a problem with the request.

BadRequestException(String) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException

400 - BAD REQUEST

BadRequestException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException

404 - BAD REQUEST

BadRequestException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException

404 - BAD REQUEST

BadTemplateException - Exception in org.intermine.api.profile

Exception thrown when template has invalid name.

BadTemplateException() - Constructor for exception org.intermine.api.profile.BadTemplateException

Constructor

BadTemplateException(String) - Constructor for exception org.intermine.api.profile.BadTemplateException

Constructor with message.

BAG - Static variable in class org.intermine.api.tag.TagTypes

Bag.

bag - Variable in class org.intermine.objectstore.query.BagConstraint

bag - Variable in class org.intermine.web.logic.widget.Widget

bag - Variable in class org.intermine.web.logic.widget.WidgetLdr

BAG_INVITES - Static variable in class org.intermine.api.bag.SharedBagManager

The name of the table to persist offers to share a bag with others.

BAG_NAME_PREFIX - Static variable in class org.intermine.web.logic.bag.BagHelper

When generating new bag names, this is used as a prefix.

BAG_QUERY_MAX_BATCH_SIZE - Static variable in class org.intermine.webservice.server.lists.ListUploadService

The maximum number of ids to query for each batch.

BAG_VALUES - Static variable in class org.intermine.api.profile.InterMineBag

name of bag values table

BagBuildController - Class in org.intermine.web.struts

Controller Action for buildBag.jsp

BagBuildController() - Constructor for class org.intermine.web.struts.BagBuildController

BagConstraint - Class in org.intermine.objectstore.query

Constrain a QueryClass or QueryEvaluable to be within a bag.

BagConstraint(QueryNode, ConstraintOp, Collection<?>) - Constructor for class org.intermine.objectstore.query.BagConstraint

Construct a BagConstraint from a Collection.

BagConstraint(QueryNode, ConstraintOp, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.BagConstraint

Construct a BagConstraint from an ObjectStoreBag.

bagConstraintTables - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

bagConstraintToString(SqlGenerator.State, StringBuffer, BagConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a BagConstraint object into a String suitable for putting on an SQL query.

BagConversionHelper - Class in org.intermine.web.logic.bag

Utility methods used when converting lists (bags) between types.

BagConverter - Class in org.intermine.web.logic.bag

BagConverter(InterMineAPI, WebConfig) - Constructor for class org.intermine.web.logic.bag.BagConverter

BagDetailsAction - Class in org.intermine.web.struts

Action that builds a PagedCollection to view a bag.

BagDetailsAction() - Constructor for class org.intermine.web.struts.BagDetailsAction

BagDetailsController - Class in org.intermine.web.struts

BagDetailsController() - Constructor for class org.intermine.web.struts.BagDetailsController

BagDoesNotExistException - Exception in org.intermine.api.profile

Exception thrown when bag is not found.

BagDoesNotExistException() - Constructor for exception org.intermine.api.profile.BagDoesNotExistException

Constructor

BagDoesNotExistException(String) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException

Constructor with message.

BagDoesNotExistException(Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException

Constructor with throwable

BagDoesNotExistException(String, Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException

Constructor with message and throwable

BagHelper - Class in org.intermine.web.logic.bag

Helper methods for bags.

BAGID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the bagid column in the osbag table.

BagManager - Class in org.intermine.api.bag

A BagManager provides access to all global and/or user bags and methods to fetch them by type, etc.

BagManager(Profile, Model) - Constructor for class org.intermine.api.bag.BagManager

The BagManager references the super user profile to fetch global bags.

bagManager - Variable in class org.intermine.api.InterMineAPI

bagManager - Variable in class org.intermine.api.query.QueryExecutor

bagManager - Variable in class org.intermine.webservice.server.core.JSONService

bagManager - Variable in class org.intermine.webservice.server.lists.ListInput

bagManager - Variable in class org.intermine.webservice.server.query.QueryToListService

BagManager.ByTagOrder - Class in org.intermine.api.bag

Compare lists based on their im:order:n tag

BagManager.ByTagOrder() - Constructor for class org.intermine.api.bag.BagManager.ByTagOrder

BagManager.CaseInsensitiveComparator - Class in org.intermine.api.bag

Lower-case key comparator

BagManager.CaseInsensitiveComparator() - Constructor for class org.intermine.api.bag.BagManager.CaseInsensitiveComparator

bagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm

bagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

BagNotFound - Exception in org.intermine.api.query

BagNotFound(String) - Constructor for exception org.intermine.api.query.BagNotFound

BagNotFound(String, Throwable) - Constructor for exception org.intermine.api.query.BagNotFound

bagOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

BagOperation - Class in org.intermine.api.bag.operations

BagOperation(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.BagOperation

BagOperationException - Exception in org.intermine.api.bag.operations

BagOperationException() - Constructor for exception org.intermine.api.bag.operations.BagOperationException

Constructor

BagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.BagOperationException

BagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException

BagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException

BagOperations - Class in org.intermine.api.bag

Perform logical operations on bags - combine bags to create new InterMineBags

BagProducer - Interface in org.intermine.api.bag.operations

Functional interface for BagOperations, so we can be all forward looking.

BagQuery - Class in org.intermine.api.bag

A class encapsulating a query used to create a bag from a collection of input identifiers.

BagQuery(BagQueryConfig, Model, String, String, String, boolean) - Constructor for class org.intermine.api.bag.BagQuery

Create a new BagQuery object.

BagQuery(BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.api.bag.BagQuery

Create a new BagQuery object for the default query - search for all key fields of the given class.

BagQueryConfig - Class in org.intermine.api.bag

Configuration for BagQuery objects.

BagQueryConfig(Map<String, List<BagQuery>>, Map<String, List<BagQuery>>, Map<String, Set<AdditionalConverter>>) - Constructor for class org.intermine.api.bag.BagQueryConfig

Create a new BagQueryConfig object.

bagQueryConfig - Variable in class org.intermine.api.InterMineAPI

BagQueryHandler - Class in org.intermine.api.bag

Handler for bag-query.xml files.

BagQueryHandler(Model) - Constructor for class org.intermine.api.bag.BagQueryHandler

Create a new BagQueryHandler object.

BagQueryHelper - Class in org.intermine.api.bag

BagQueryResult - Class in org.intermine.api.bag

Class to hold the results of querying for a bag of objects.

BagQueryResult() - Constructor for class org.intermine.api.bag.BagQueryResult

BagQueryResult.IssueResult - Class in org.intermine.api.bag

Simple struct to hold three pieces of information together.

BagQueryResult.IssueResult(String, String, List) - Constructor for class org.intermine.api.bag.BagQueryResult.IssueResult

BagQueryRunner - Class in org.intermine.api.bag

For a given list of input strings search for objects using default and configured queries for a particular type.

BagQueryRunner(ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, TemplateManager) - Constructor for class org.intermine.api.bag.BagQueryRunner

Construct with configured bag queries and a map of type -> key fields.

bagQueryRunner - Variable in class org.intermine.api.InterMineAPI

bagQueryRunner - Variable in class org.intermine.api.query.QueryExecutor

BagQueryUpgrade - Class in org.intermine.api.bag

BagQueryUpgrade(BagQueryRunner, InterMineBag) - Constructor for class org.intermine.api.bag.BagQueryUpgrade

BagResultCategoryKeyFormatter - Class in org.intermine.webservice.server.idresolution

Format a bag query result, grouping by category of issue.

BagResultCategoryKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter

BagResultFormatter - Interface in org.intermine.webservice.server.idresolution

BagResultOutputKeyFormatter - Class in org.intermine.webservice.server.idresolution

Format a bag result grouping by matched object.

BagResultOutputKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter

BagSet - Class in org.intermine.api.profile

A class containing valiud and invalid bags.

BagSet(Map<String, InterMineBag>, Map<String, InvalidBag>) - Constructor for class org.intermine.api.profile.BagSet

Constructor

BagState - Enum in org.intermine.api.profile

Enumeration for describing the state of a bag: current not current (= the upgrading process has not been executed yet) upgrading (= the upgrading process is upgrading it) to upgrade (= the upgrading process has not been able to upgrade it because there are some conflicts that the user has to solve manually ))

bagTablesInDatabase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

bagTablesToRemove - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

BagUpgradeAction - Class in org.intermine.web.struts

An action that prepare a BagQueryResult and save it into the session.

BagUpgradeAction() - Constructor for class org.intermine.web.struts.BagUpgradeAction

BagUploadConfirmAction - Class in org.intermine.web.struts

Action class for saving a bag from the bagUploadConfirm page into the user profile.

BagUploadConfirmAction() - Constructor for class org.intermine.web.struts.BagUploadConfirmAction

BagUploadConfirmController - Class in org.intermine.web.struts

Controller for the bagUploadConfirm; retrieve an IDResolutionService job id

BagUploadConfirmController() - Constructor for class org.intermine.web.struts.BagUploadConfirmController

BagUploadConfirmForm - Class in org.intermine.web.struts

Form for the bagUploadConfirm page.

BagUploadConfirmForm() - Constructor for class org.intermine.web.struts.BagUploadConfirmForm

Constructor

BagUploadConfirmInlineResultsTable - Class in org.intermine.web.logic.results

An inline table of ResultElements used ob BagUploadConfirm At the moment, we use this custom class to create a custom type of table row that will be extended with identifier and rowspan attributes needed on list upload confirmation step

BagUploadConfirmInlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable

Construct a new InlineResultsTable object

BagUploadConfirmInlineResultsTableRow - Class in org.intermine.web.logic.results

Used on BagUploadConfirmIssueController (List upload confirm step) to add an identifier the user was trying to resolve with the number of rows in the ResultsTable corresponding to the said identifier.

BagUploadConfirmInlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

BagUploadConfirmIssueController - Class in org.intermine.web.struts

Controller for the bagUploadConfirmIssue tile.

BagUploadConfirmIssueController() - Constructor for class org.intermine.web.struts.BagUploadConfirmIssueController

BAGVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the value column in the osbag table.

BagValue - Class in org.intermine.api.profile

A class representing a value stored in an InterMineBag.

BagValue(String, String) - Constructor for class org.intermine.api.profile.BagValue

Constructor

bagValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

Base64PublicKeyDecoder - Class in org.intermine.web.security

A public key decoder that reads public keys encoded as base64 strings.

Base64PublicKeyDecoder() - Constructor for class org.intermine.web.security.Base64PublicKeyDecoder

Construct a new decoder.

BaseDisclosureTag - Class in org.intermine.web.tags.disclosure

Base tag handler from which are all disclosure tag handlers derived.

BaseDisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.BaseDisclosureTag

BaseEquivalentObjectFetcher - Class in org.intermine.dataloader

Class providing methods to look up equivalent objects by primary key in a production objectstore.

BaseEquivalentObjectFetcher(Model, IntToIntMap, ObjectStore) - Constructor for class org.intermine.dataloader.BaseEquivalentObjectFetcher

Constructor for this EquivalentObjectFetcher.

BASIC_FORMATS - Static variable in enum org.intermine.webservice.server.Format

The basic formats: HTML, TEXT, XML, JSON

batch - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Batch - Class in org.intermine.sql.writebatch

A class representing a collection of writes to an SQL database.

Batch(BatchWriter) - Constructor for class org.intermine.sql.writebatch.Batch

Constructs an empty Batch, with no tables.

BATCH_SIZE - Static variable in class org.intermine.api.config.Constants

Batch size for the underlying objectstore

BATCH_SIZE - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

BATCH_SIZE - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

BATCH_SIZE - Static variable in class org.intermine.webservice.server.query.result.QueryResultService

Batch size to use

batchCommit(Connection) - Method in class org.intermine.sql.writebatch.Batch

Flushes the batch out to the database server, then commits and re-opens the transaction, but does not guarantee that the operation is finished when this method returns.

batchCommitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.

batchCommitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.

batchCommitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.

batchCommitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Commits a transaction and opens a new one, without guaranteeing the operation is finished before this method returns.

batches - Variable in class org.intermine.objectstore.query.ResultsBatches

batchesCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

BatchingFetcher - Class in org.intermine.dataloader

Class providing EquivalentObjectFetcher functionality that batches fetches to improve performance.

BatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.BatchingFetcher

Constructor

batchQueried - Variable in class org.intermine.dataloader.BatchingFetcher

batchSize - Variable in class org.intermine.objectstore.query.ResultsBatches

BatchWriter - Interface in org.intermine.sql.writebatch

An interface representing an object that can flush a TableBatch to an SQL server Connection.

BatchWriterPostgresCopyImpl - Class in org.intermine.sql.writebatch

An implementation of the BatchWriter interface that uses PostgreSQL-specific COPY commands.

BatchWriterPostgresCopyImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

BatchWriterPreparedStatementImpl - Class in org.intermine.sql.writebatch

An implementation of the BatchWriter interface that uses JDBC PreparedStatement addBatch() and executeBatch() methods.

BatchWriterPreparedStatementImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl

BatchWriterSimpleImpl - Class in org.intermine.sql.writebatch

An implementation of the BatchWriter interface that uses simple JDBC addBatch() and executeBatch() methods.

BatchWriterSimpleImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterSimpleImpl

BEDRecord - Class in org.intermine.bio.io.bed

A record in a BED formatted file.

BEDRecord(String, int, int, String, int, String) - Constructor for class org.intermine.bio.io.bed.BEDRecord

Constructor The following five attributes are normally hosted in InterMine cases.

BEDUtil - Class in org.intermine.bio.web.export

Utility methods for UCSC BED format.

BeginAction - Class in org.intermine.web.struts

Prepare templates and news to be rendered on home page

BeginAction() - Constructor for class org.intermine.web.struts.BeginAction

beginTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Request that the ObjectStore begins a transaction, delegate to internal ObjectStoreWriter.

beginTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Request that the ObjectStoreWriter begins a transaction

beginTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Request that the ObjectStoreWriter begins a transaction

beginTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Begins a transaction.

beof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

bestCandidate - Variable in class org.intermine.sql.precompute.BestQueryExplainer

BestQuery - Class in org.intermine.sql.precompute

This object is an abstract superclass for a Best Query tracker.

BestQuery() - Constructor for class org.intermine.sql.precompute.BestQuery

BestQueryException - Exception in org.intermine.sql.precompute

An Exception that may be thrown by an BestQuery.

BestQueryException() - Constructor for exception org.intermine.sql.precompute.BestQueryException

Constructs an BestQueryException

BestQueryException(String) - Constructor for exception org.intermine.sql.precompute.BestQueryException

Constructs an BestQueryException with the specified detail message.

BestQueryException(Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException

Constructs an BestQueryException with the specified nested throwable.

BestQueryException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException

Constructs an BestQueryException with the specified detail message and nested throwable.

BestQueryExplainer - Class in org.intermine.sql.precompute

Gets the database to explain each Query added and keeps hold of the best one so far.

BestQueryExplainer() - Constructor for class org.intermine.sql.precompute.BestQueryExplainer

Constructs an empty BestQueryExplainer for testing purposes

BestQueryExplainer(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer

Constructs a BestQueryExplainer that will use the given Connection to explain Queries.

BestQueryExplainer.Candidate - Class in org.intermine.sql.precompute

A class representing a candidate optimised query.

BestQueryExplainer.Candidate(String) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Constructor.

BestQueryExplainer.Candidate(Query) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Constructor.

BestQueryExplainerVerbose - Class in org.intermine.sql.precompute

Gets the database to explain each Query added and keeps hold of the best one, logging all actions for the benefit of the IqlShell user.

BestQueryExplainerVerbose(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainerVerbose

Constructs an empty BestQueryExplainerVerbose.

BestQueryFallback - Class in org.intermine.sql.precompute

Gets the database to explain each Query added and keeps hold of the best one so far.

BestQueryFallback(Query, String) - Constructor for class org.intermine.sql.precompute.BestQueryFallback

Constructs a BestQueryFallback

BestQueryLogger - Class in org.intermine.sql.precompute

Logs each query added.

BestQueryLogger(boolean) - Constructor for class org.intermine.sql.precompute.BestQueryLogger

Constructs a BestQueryLogger

BestQueryStorer - Class in org.intermine.sql.precompute

Stores each query added.

BestQueryStorer() - Constructor for class org.intermine.sql.precompute.BestQueryStorer

Constructs a BestQueryStorer

bestQueryString - Variable in class org.intermine.sql.precompute.BestQueryLogger

betterThan(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Returns true if the argument is slower than this, or if the argument is null.

BIG_BATCH_SIZE - Static variable in class org.intermine.api.results.WebResults

The batch size to use when we need to iterate through the whole result set.

BIG_BATCH_SIZE - Static variable in class org.intermine.web.struts.SaveBagAction

The batch size to use when we need to iterate through the whole result set.

BioConverterUtil - Class in org.intermine.bio.util

Helper class for data converters.

BioDBConverter - Class in org.intermine.bio.dataconversion

A DBConverter with helper methods for bio sources.

BioDBConverter(Database, Model, ItemWriter, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDBConverter

Create a new BioDBConverter object.

BioDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.BioDBConverter

Create a new BioDBConverter object.

BioDirectoryConverter - Class in org.intermine.bio.dataconversion

A DirectoryConverter that automatically sets the dataSets collection of objects as they are stored.

BioDirectoryConverter(ItemWriter, Model, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDirectoryConverter

Create a new BioDirectoryConverter.

BioDirectoryConverter(ItemWriter, Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDirectoryConverter

Create a new BioDirectoryConverter.

BioFileConverter - Class in org.intermine.bio.dataconversion

A FileConverter that automatically sets the dataSets collection of objects as they are stored.

BioFileConverter(ItemWriter, Model, String, String) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter

Create a new BioFileConverter.

BioFileConverter(ItemWriter, Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter

Create a new BioFileConverter.

BioFileConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter

Create a new BioFileConverter.

BioGridConverter - Class in org.intermine.bio.dataconversion

DataConverter to parse biogrid data into items Genetic interactions are labeled protein interactions, so we can't store or create any objects until all experiments and interactors are processed.

BioGridConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.BioGridConverter

Constructor

BioGridConverter.Config - Class in org.intermine.bio.dataconversion

Represents configuration for a specific organism

BioGridConverter.Config() - Constructor for class org.intermine.bio.dataconversion.BioGridConverter.Config

BioGridConverter.ExperimentHolder - Class in org.intermine.bio.dataconversion

Holder object for Experiment.

BioGridConverter.ExperimentHolder() - Constructor for class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

BioQueries - Class in org.intermine.bio.util

Bio utility methods for queries.

BioStoreHook - Class in org.intermine.bio.dataconversion

An implementation of DataConverterStoreHook that adds DataSet and DataSource references and collections to Items as they are stored.

BioStoreHook(Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioStoreHook

Create a new DataSetStoreHook object.

BioStoreHook(Model, String) - Constructor for class org.intermine.bio.dataconversion.BioStoreHook

Create a new DataSetStoreHook object.

BioUtil - Class in org.intermine.bio.util

Utility methods for the flymine package.

BOOLEAN_KEYS - Static variable in class org.intermine.api.profile.UserPreferences

Common keys

BOOLEAN_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint

BOTH_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as being both false.

BOTH_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as being both true.

BrandingService - Class in org.intermine.webservice.server.branding

Serve branding information so that a client can provide a branded visual experience.

BrandingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.branding.BrandingService

broken - Variable in class org.intermine.dataloader.DataTracker

BuildBagAction - Class in org.intermine.web.struts

An action that makes a bag from text.

BuildBagAction() - Constructor for class org.intermine.web.struts.BuildBagAction

BuildBagForm - Class in org.intermine.web.struts

Form bean to represent the inputs needed to create a bag from user input.

BuildBagForm() - Constructor for class org.intermine.web.struts.BuildBagForm

BuildDbTask - Class in org.intermine.task

Generates and inserts SQL given database name, schema and temporary directory

BuildDbTask() - Constructor for class org.intermine.task.BuildDbTask

buildFromComponent(SqlGenerator.State, Query, DatabaseSchema, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds the FROM list for the SQL query.

buildGroupBy(Query, DatabaseSchema, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds a String representing the GROUP BY component of the Sql query.

buildIndex(ObjectStore) - Method in class org.intermine.web.autocompletion.AutoCompleter

Build the index from the database blob

buildKeyStore() - Method in class org.intermine.web.security.KeyStoreBuilder

Build the key store.

buildObject(ResultSet, String, ObjectStoreInterMineImpl, Class<?>, Set<String>) - Static method in class org.intermine.objectstore.intermine.ResultsConverter

Builds an object from separate fields in flat mode.

buildOrderBy(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds a String representing the ORDER BY component of the Sql query.

buildQueryValue(PathConstraint) - Method in class org.intermine.web.logic.widget.WidgetLdr

Return a QueryValue instance using the path contraint given in input

buildSelectComponent(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds a String representing the SELECT component of the Sql query.

buildTree(String) - Method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder

Recurse through the model and build a tree of metadata nodes based on this

buildWhereClause(SqlGenerator.State, Query, Constraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds the WHERE clause for the SQL query.

C

cache - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

CACHE_LARGEST_OBJECT - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

CacheHoldingArrayList<E> - Class in org.intermine.util

This is an extension of the the ArrayList class, designed to be used by systems that return Lists of data, with extra data that should not be flushed out of a cache until the List is garbage collected.

CacheHoldingArrayList() - Constructor for class org.intermine.util.CacheHoldingArrayList

Empty constructor

CacheHoldingArrayList(Collection<E>) - Constructor for class org.intermine.util.CacheHoldingArrayList

Constructs a new instance from another Collection.

CacheHoldingArrayList(int) - Constructor for class org.intermine.util.CacheHoldingArrayList

Constructs a new instance with the given initial capacity.

cacheLines - Variable in class org.intermine.sql.precompute.OptimiserCache

A Map that holds a mapping from unoptimised query string (with LIMIT and OFFSET stripped off) to a Set of OptimiserCacheLine objects.

cacheLinks(MultiKey, Collection<PartnerLink>) - Method in class org.intermine.api.mines.FriendlyMineManager

CacheMap<K,V> - Class in org.intermine.util

This is a Map implementation designed specifically for people intending to create a cache.

CacheMap(int, float) - Constructor for class org.intermine.util.CacheMap

Constructs a new, empty CacheMap with the given initial capacity and the given load factor.

CacheMap(int) - Constructor for class org.intermine.util.CacheMap

Constructs a new, empty CacheMap with the given initial capacity and the default load factor, which is 0.75.

CacheMap() - Constructor for class org.intermine.util.CacheMap

Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75).

CacheMap(String) - Constructor for class org.intermine.util.CacheMap

Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75), and a name.

CacheMap(Map<K, V>) - Constructor for class org.intermine.util.CacheMap

Constructs a new CacheMap with the same mappings as the specified Map.

cacheMisses - Variable in class org.intermine.dataloader.BatchingFetcher

cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Places an entry into the objectstore getObjectById cache.

cacheObjectById(Integer, InterMineObject) - Method in interface org.intermine.objectstore.ObjectStore

Places an entry into the objectstore getObjectById cache.

cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Places an entry into the objectstore getObjectById cache.

cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Places an entry into the objectstore getObjectById cache.

calculate(EnrichmentInput, Double, String, boolean, CorrectionCoefficient) - Static method in class org.intermine.web.logic.widget.EnrichmentCalculation

Perform an enrichment calculation based on input from some source and return results that include a p-value and count for each attribute that was observed in the sample.

CalculateLocations - Class in org.intermine.bio.postprocess

Calculate additional mappings between annotation after loading into genomic ObjectStore.

CalculateLocations(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CalculateLocations

Create a new CalculateLocations object from an ObjectStoreWriter

CalculateLocations.SimpleLoc - Class in org.intermine.bio.postprocess

Lightweight representation of a Location for easier manipulation and storing in maps.

CalculateLocations.SimpleLoc(int, int, int, int, String) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Construct with integer values

CalculateLocations.SimpleLoc(int, int, Location) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Construct with integer values for object and subject and a Location object

call(Either<A, B>) - Method in class org.intermine.webservice.server.core.EitherVisitor

call(A) - Method in class org.intermine.webservice.server.core.F

The body of the function

call(X) - Method in class org.intermine.webservice.server.core.F.Constant

Call this function, returning the value supplied to the constructor.

call(A) - Method in interface org.intermine.webservice.server.core.Function

Take an A and return a B.

call(T) - Method in interface org.intermine.webservice.server.core.Predicate

Apply some test to some kind of thing.

call(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory

Callback - Class in org.intermine.web.struts.oauth2

The controller that handles the requests made after the user has visited their authorisation provider to log-in.

Callback() - Constructor for class org.intermine.web.struts.oauth2.Callback

CALLBACK_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

The callback to be supplied for jsonp calls

canAssignObjectToType(Class<?>, InterMineObject) - Static method in class org.intermine.api.util.PathUtil

Return true if given type (of a constraint) can be assigned to the InterMineObject - i.e.

cancelRequest(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

This method cancels any Statement running in a given request ID, and blacklists that ID.

candidates - Variable in class org.intermine.sql.precompute.BestQueryExplainer

candidateTables - Variable in class org.intermine.sql.precompute.BestQueryExplainer

canDoPkNow(PrimaryKey, ClassDescriptor, Map<PrimaryKey, ClassDescriptor>) - Method in class org.intermine.dataloader.BatchingFetcher

Returns whether this primary key can be fetched now.

canExport(List<Class<?>>) - Method in interface org.intermine.web.logic.export.Exporter

This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.

canExport(List<Class<?>>) - Method in class org.intermine.web.logic.export.ExporterImpl

This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.

canExport(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper

Return true if the specified class or a subclass is found in a column of the paged table (or is the parent class of a field displayed in the table).

canExport(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter

canExport(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter

Check if this TableExporter can export the given PagedTable.

canHaveCollection(String) - Method in class org.intermine.xml.full.Item

Return true if and only if the argument names a possible collection for this Item.

canHaveReference(String) - Method in class org.intermine.xml.full.Item

Return true if and only if the argument names a possible reference for this Item.

canonicaliseIndexes(Collection<String>) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager

Takes a collection of index strings, and removes redundant entries.

canServe(Format) - Method in class org.intermine.webservice.server.lists.AvailableListsService

canServe(Format) - Method in class org.intermine.webservice.server.lists.ListMakerService

canServe(Format) - Method in class org.intermine.webservice.server.model.ModelService

canServe(Format) - Method in class org.intermine.webservice.server.path.PossibleValuesService

canServe(Format) - Method in class org.intermine.webservice.server.query.CodeService

canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRemovalService

canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRetrieverService

canServe(Format) - Method in class org.intermine.webservice.server.query.QueryToListService

canServe(Format) - Method in class org.intermine.webservice.server.query.QueryUploadService

canServe(Format) - Method in class org.intermine.webservice.server.query.result.QueryResultService

canServe(Format) - Method in class org.intermine.webservice.server.query.result.TableRowService

canServe(Format) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService

canServe(Format) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService

canServe(Format) - Method in class org.intermine.webservice.server.template.SingleTemplateService

canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateRemovalService

canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateUploadService

canServe(Format) - Method in class org.intermine.webservice.server.VersionService

canServe(Format) - Method in class org.intermine.webservice.server.WebService

Check whether the format is acceptable.

canServe(Format) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

castBagsToCommonType(Collection<InterMineBag>, String, Set<String>, Profile, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

Given a common type, return a collection of bags cast to that type.

CATEGORIES - Static variable in class org.intermine.web.logic.Constants

ServletContext attribute, List of category names.

categoriseBasedOnTags(FieldDescriptor, String, DisplayField, Map<String, DisplayField>, TagManager, String, Map<String, Map<String, DisplayField>>, boolean) - Static method in class org.intermine.web.struts.ReportController

For a given FieldDescriptor, look up its 'aspect:' tags and place it in the correct map within placementRefsAndCollections.

category - Variable in class org.intermine.sql.precompute.PrecomputedTable

caughtError - Variable in class org.intermine.bio.dataconversion.IdResolverFactory

CEIL - Static variable in class org.intermine.objectstore.query.QueryFunction

Smallest integer value greater than input.

ChadoCV - Class in org.intermine.bio.chado

Objects of this class represent a controlled vocabulary from chado.

ChadoCV(String) - Constructor for class org.intermine.bio.chado.ChadoCV

Create a new ChadoCV.

ChadoCVFactory - Class in org.intermine.bio.chado

A factory for ChadoCV objects.

ChadoCVFactory(Connection) - Constructor for class org.intermine.bio.chado.ChadoCVFactory

Create a new ChadoCVFactory.

ChadoCVTerm - Class in org.intermine.bio.chado

Objects of this class represent one row of the chado cvterm table.

ChadoCVTerm(String) - Constructor for class org.intermine.bio.chado.ChadoCVTerm

Create a new cv term object

ChadoDBConverter - Class in org.intermine.bio.dataconversion

DataConverter to read from a Chado database into items

ChadoDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.ChadoDBConverter

Create a new ChadoDBConverter object.

ChadoProcessor - Class in org.intermine.bio.dataconversion

A processor for a chado module.

ChadoProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.ChadoProcessor

Create a new ChadoModuleProcessor object.

ChangeEvent - Interface in org.intermine.api.search

Events that represent changes in something.

ChangePasswordAction - Class in org.intermine.web.struts

ChangePasswordAction() - Constructor for class org.intermine.web.struts.ChangePasswordAction

ChangePasswordForm - Class in org.intermine.web.struts

Form bean to represent the inputs needed to change a password from user input.

ChangePasswordForm() - Constructor for class org.intermine.web.struts.ChangePasswordForm

changePasswordWithToken(String, String) - Method in class org.intermine.api.profile.ProfileManager

Changes the password of a profile if the given token is valid.

changePath(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Change the currently active metadata Node

changeSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Increments the sequence numbers for the given set of database components.

ChangeTableAction - Class in org.intermine.web.struts

Implementation of DispatchAction.

ChangeTableAction() - Constructor for class org.intermine.web.struts.ChangeTableAction

ChangeTableSizeAction - Class in org.intermine.web.struts

Changes the size of the results displayed.

ChangeTableSizeAction() - Constructor for class org.intermine.web.struts.ChangeTableSizeAction

ChangeTableSizeForm - Class in org.intermine.web.struts

Form bean for changing the page size.

ChangeTableSizeForm() - Constructor for class org.intermine.web.struts.ChangeTableSizeForm

Constructor

changeViewPathDescription(String, String) - Method in class org.intermine.dwr.AjaxServices

Set the description of a view path.

characters(char[], int, int) - Method in class org.intermine.api.bag.BagQueryHandler

characters(char[], int, int) - Method in class org.intermine.api.bag.InvitationHandler

characters(char[], int, int) - Method in class org.intermine.api.profile.PreferencesHandler

characters(char[], int, int) - Method in class org.intermine.pathquery.PathQueryHandler

characters(char[], int, int) - Method in class org.intermine.webservice.server.ServiceListingHandler

charAt(int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Return a character from the specified index.

charAt(int) - Method in class org.intermine.objectstore.query.ClobAccess

Return a character from the specified index.

charAt(int) - Method in class org.intermine.objectstore.query.PendingClob

Return a character from the specified index.

check(Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.precompute.OptimiserMappingChecker

Checks a partial mapping.

check(Map<T, T>) - Method in interface org.intermine.util.MappingUtilChecker

Checks a partial mapping.

checkAttribute(String) - Method in class org.intermine.xml.full.Item

Return true if the name parameter is an attribute of the class for this Item or if the Model or the className of this Item haven't been set.

checkCollection(String) - Method in class org.intermine.xml.full.Item

Throw a RuntimeException if the name parameter isn't an collection in the class set by setClassName() in the Model set by setModel().

checkComparisonEquals(int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take an integer as if it was created by compare, and return true if this implies that the left constraint is EQUAL to the right constraint, in a loose sense.

checkComparisonImplies(int) - Static method in class org.intermine.sql.query.AbstractConstraint

Take an integer as if it was created by compare, and return true if this implies that the left constraint IMPLIES the right constraint, in a loose sense.

checkFieldExists(Model, String, String, String) - Static method in class org.intermine.bio.postprocess.PostProcessUtil

Check that a class exists and has a field of the given name.

CheckForIsNotNullConstraint - Class in org.intermine.objectstore.intermine

For use with ConstraintHelper.traverseConstraints().

CheckForIsNotNullConstraint(QueryNode) - Constructor for class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint

Construct with the QueryNode to test for NOT NULL constraint.

checkImplementations(String) - Method in class org.intermine.xml.full.Item

Throw RuntimeException if the given implementations don't match the model.

checkLists(Map<String, InterMineBag>, List<String>) - Method in class org.intermine.webservice.server.lists.ListInput

Make sure that any lists names exist.

checkPassword(String, String) - Static method in class org.intermine.util.PasswordHasher

Checks to see if a password matches an optionally hashed password entry.

checkPathFormat(String) - Static method in class org.intermine.pathquery.PathQuery

Verifies the format of a path for a query.

checkReference(String) - Method in class org.intermine.xml.full.Item

Throw a RuntimeException if the name parameter isn't an reference in the class set by setClassName() in the Model set by setModel().

checkResponse() - Method in class org.intermine.webservice.client.util.HttpConnection

Called to check the response and generate an appropriate exception (on failure).

checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Checks a number against the sequence number, and throws an exception if they do not match.

checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Checks a number against the sequence number, and throws an exception if they do not match.

checkStartLimit(int, int, Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Checks the start and limit to see whether they are inside the hard limits for this ObjectStore

checkTaxonId(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Check that the given taxon id has some data for it. if an exception thrown, there must be something wrong with resolver factory.

ChromosomeLocationHelper - Class in org.intermine.bio.query.range

Method to help querying for ranges

ChromosomeLocationHelper() - Constructor for class org.intermine.bio.query.range.ChromosomeLocationHelper

Method to set up chromosome fields for helping

CLASS - Static variable in class org.intermine.api.tag.TagTypes

A Class/ClassDescriptor.

CLASS_KEYS - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key to use to store the class_keys.properties file.

ClassChooserController - Class in org.intermine.web.struts

Gets list of help text blurbs for each class, and passes them on to the display page.

ClassChooserController() - Constructor for class org.intermine.web.struts.ClassChooserController

ClassConstraint - Class in org.intermine.objectstore.query

Constrain whether a QueryClass is equal/not equal to another QueryClass or an example of an object belonging to a QueryClass.

ClassConstraint(QueryClass, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ClassConstraint

Construct ClassConstraint

ClassConstraint(QueryClass, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ClassConstraint

Construct ClassConstraint

classConstraintToString(SqlGenerator.State, StringBuffer, ClassConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a ClassConstraint object into a String suitable for putting in an SQL query.

ClassKeyHelper - Class in org.intermine.api.config

Methods to read and manage keys for classes.

classKeys - Variable in class org.intermine.api.InterMineAPI

ClassKeys - Interface in org.intermine.api.types

Type alias for classkeys - simplifies matters and prevents mistakes.

ClassKeyServlet - Class in org.intermine.webservice.server

A Servlet for routing requests to the ClassKeyService.

ClassKeyServlet() - Constructor for class org.intermine.webservice.server.ClassKeyServlet

ClassKeysNotFoundException - Exception in org.intermine.api.bag

Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.

ClassKeysNotFoundException(String) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException

Constructs an IncompatibleBagTypesException with the specified detail message.

ClassKeysNotFoundException(Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException

Constructs an IncompatibleBagTypesException with the specified nested throwable.

ClassKeysNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException

Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.

ClassKeysService - Class in org.intermine.webservice.server

A service to fetch a JSON representation of class keys for all classes in the model.

ClassKeysService(InterMineAPI) - Constructor for class org.intermine.webservice.server.ClassKeysService

Construct with the InterMineAPI.

className - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput

className - Variable in class org.intermine.web.struts.QueryClassSelectForm

classNotExists(Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.EquivalentObjectHints

Returns true if there were no instances of the given class in the database.

ClassResourceOpener - Class in org.intermine.web.logic

Objects that open resources relative to a classpath.

ClassResourceOpener(Class<?>) - Constructor for class org.intermine.web.logic.ClassResourceOpener

Constructor.

classToType(Class<?>) - Static method in class org.intermine.objectstore.query.UnknownTypeValue

Converts a Class into an approximate type.

clean() - Method in class org.intermine.dataloader.ObjectDescription

Marks the ObjectDescription as clean - that is all the data has been flushed to the backing database.

cleanTags(TagManager) - Static method in class org.intermine.web.struts.InitialiserPlugin

Remove class tags from the user profile that refer to classes that non longer exist

cleanUp() - Method in class org.intermine.webservice.server.WebService

Subclasses may put clean-up code here, to be run after the request has been executed.

clear() - Method in class org.intermine.api.profile.UserPreferences

clear() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Remove all items held locally in handler.

clear() - Method in class org.intermine.dataloader.DataTracker

Clears the data tracker of all entries.

clear() - Method in class org.intermine.sql.writebatch.Batch

Clears the batch without writing it to the database.

clear() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Clears the batch.

clear() - Method in interface org.intermine.sql.writebatch.Table

Clears the batch.

clear() - Method in class org.intermine.sql.writebatch.TableBatch

Clears the batch.

clear() - Method in class org.intermine.util.AlwaysMap

clear() - Method in class org.intermine.util.IdentityMap

clear() - Method in class org.intermine.util.IntPresentSet

Removes all ints from the object.

clear() - Method in class org.intermine.util.IntToIntMap

Removes all mappings from the object.

clear() - Method in class org.intermine.util.PseudoSet

clear() - Method in class org.intermine.util.ReferenceMap

clear() - Method in class org.intermine.webservice.client.results.ResultRowList

clearCache() - Method in class org.intermine.webservice.client.core.Service

Clear the cache on this object.

clearCache() - Method in class org.intermine.webservice.client.services.ModelService

clearConstraints() - Method in class org.intermine.pathquery.PathQuery

Clears the entire set of constraints from this query, and resets the constraint logic.

clearConstraints() - Method in class org.intermine.template.TemplateQuery

Clears the entire set of constraints from this query, and resets the constraint logic.

clearDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Reset the list of DataSet items.

clearDescriptions() - Method in class org.intermine.pathquery.PathQuery

Removes all path descriptions from this query.

clearFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Clear the list of final items.

clearLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Clear the location item for this record.

clearObj(Integer) - Method in class org.intermine.dataloader.DataTracker

Clears the cache for a particular object, in preparation for writing all the data for that object.

clearOrderBy() - Method in class org.intermine.objectstore.query.Query

Clears the ORDER BY clause of this Query

clearOrderBy() - Method in class org.intermine.pathquery.PathQuery

Clears the entire order by list.

clearOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery

Clears all outer join status data from this query.

clearProblem() - Method in class org.intermine.sql.writebatch.Batch

Clears the problem with the Batch.

clearPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Reset the list of Publication items.

clearSelect() - Method in class org.intermine.objectstore.query.Query

Clears the SELECT list

clearSelectIds() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Clear the table selection

clearView() - Method in class org.intermine.pathquery.PathQuery

Clears the entire view list.

Clob - Class in org.intermine.objectstore.query

Object representing a large String that has been stored in the database.

Clob(int) - Constructor for class org.intermine.objectstore.query.Clob

Constructs a new Clob.

clob - Variable in class org.intermine.objectstore.query.ClobAccess

CLOB_PAGE_SIZE - Static variable in class org.intermine.objectstore.query.Clob

Page size for clob data

CLOB_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the table that stores Clobs.

ClobAccess - Class in org.intermine.objectstore.query

Class used to read a Clob from the ObjectStore.

ClobAccess() - Constructor for class org.intermine.objectstore.query.ClobAccess

Protected constructor for use by PendingClob only.

ClobAccess(ObjectStore, Clob) - Constructor for class org.intermine.objectstore.query.ClobAccess

Construct a ClobAccess object from an ObjectStore and a Clob.

ClobAccess.ClobAccessSubclassFactory - Class in org.intermine.objectstore.query

Class to provide fast access to the constructor of plugin subclasses of ClobAccess.

ClobAccess.ClobAccessSubclassFactory() - Constructor for class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory

ClobAccessReverseComplement - Class in org.intermine.bio.util

Subclass of ClobAccess that reverses and complements the DNA sequence contained within it.

ClobAccessReverseComplement(ClobAccess) - Constructor for class org.intermine.bio.util.ClobAccessReverseComplement

Construct this object from an existing ClobAccess object

CLOBID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the clobid column in the clob table.

CLOBPAGE_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the page number column in the clob table.

CLOBVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the value column in the clob table.

clone() - Method in class org.intermine.api.profile.InterMineBag

Create copy of bag.

clone() - Method in class org.intermine.api.template.ApiTemplate

Clone this ApiQuery

clone() - Method in class org.intermine.pathquery.PathQuery

Returns a deep copy of this object.

clone() - Method in class org.intermine.template.TemplateQuery

Clone this TemplateQuery.

cloneAttributeDescriptors(Set<AttributeDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

Clone a set of AttributeDescriptors.

cloneClassDescriptor(ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger

Construct a ClassDescriptor that takes on all the properties of cld without attaching to a particular Model.

cloneCollectionDescriptors(Set<CollectionDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

Clone a set of CollectionDescriptors.

cloneInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil

Create a clone of given InterMineObject including the id.

cloneQuery(Query) - Static method in class org.intermine.objectstore.query.QueryCloner

Clones a query object.

cloneReferenceDescriptors(Set<ReferenceDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

Clone a set of ReferenceDescriptors.

cloneWithoutEditableConstraints() - Method in class org.intermine.template.TemplateQuery

Return a clone of this template query with all editable constraints removed - i.e. a query that will return all possible results of executing the template.

close() - Method in class org.intermine.api.bag.BagManager

Close the TagManager

close() - Static method in class org.intermine.api.lucene.KeywordSearch

set all the variables to NULL

close() - Method in class org.intermine.api.profile.ProfileManager

Close this ProfileManager

close() - Method in class org.intermine.api.profile.TagManager

Close this TagManager.

close() - Method in class org.intermine.api.tracker.TrackerDelegate

Release the db connection when done.

close() - Method in class org.intermine.bio.dataconversion.BioGridConverter

Perform any necessary clean-up after processing

close() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Perform any necessary clean-up after post-conversion

close() - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter

Perform any necessary clean-up after processing

close() - Method in class org.intermine.dataconversion.DataConverter

Perform any necessary clean-up after processing

close() - Method in class org.intermine.dataconversion.DirectoryConverter

Perform any necessary clean-up after post-conversion

close() - Method in interface org.intermine.dataconversion.ItemWriter

Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.

close() - Method in class org.intermine.dataconversion.MockItemWriter

Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.

close() - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.

close(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Close method - prints out summary data.

close(Source) - Method in class org.intermine.dataloader.BatchingFetcher

Close method - prints out summary data.

close() - Method in class org.intermine.dataloader.DataTracker

Closes this DataTracker, releasing both connections to the database.

close() - Method in class org.intermine.dataloader.DirectDataLoader

Close the DirectDataLoader, must be called to make sure final batch of data is stored.

close(Source) - Method in class org.intermine.dataloader.HintingFetcher

Close method - prints out summary data.

close() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Closes the connection associated with this ObjectStoreWriter

close() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Closes the connection associated with this ObjectStoreWriter

close(Source) - Method in class org.intermine.dataloader.ParallelBatchingFetcher

Close method - prints out summary data.

close() - Method in class org.intermine.dataloader.XmlDataLoader

Perform any necessary clean-up and close the integration writer

close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream

close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream

close() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Closes this ObjectStore's DB log connection.

close() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Closes this ObjectStore's DB log connection.

close() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Closes the connection associated with this ObjectStoreWriter

close() - Method in class org.intermine.sql.logging.DatabaseWriter

Close this Writer

close(Connection) - Method in class org.intermine.sql.writebatch.Batch

Closes this BatchWriter.

close() - Method in class org.intermine.webservice.client.util.HttpConnection

Closes connection.

closeIndexWriter() - Method in class org.intermine.web.autocompletion.LuceneIndex

close the current indexWriter

closeSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

cls - Variable in class org.intermine.objectstore.query.ContainsConstraint

cls - Variable in class org.intermine.objectstore.query.SubqueryConstraint

clsCol - Variable in class org.intermine.bio.dataconversion.IdResolverFactory

clsName - Variable in class org.intermine.task.AnalyseDbTask

clsName - Variable in class org.intermine.task.DirectoryConverterTask

clsName - Variable in class org.intermine.task.FileConverterTask

clsName - Variable in class org.intermine.task.PostProcessorTask

COALESCE - Static variable in class org.intermine.sql.query.Function

COALESCE operator - used by the precomputed tables' orderby fields.

CodeService - Class in org.intermine.webservice.server.query

A service for generating code based on a query.

CodeService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.CodeService

Constructor.

CodeServlet - Class in org.intermine.webservice.server.query

A servlet for routing requests to the code service.

CodeServlet() - Constructor for class org.intermine.webservice.server.query.CodeServlet

CodeTranslator - Class in org.intermine.webservice.server

Translates strings between codes used in ConstraintOp class and abbreviations or full code names of operations.

collapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction

Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).

COLLECTION - Static variable in class org.intermine.api.tag.TagTypes

Collection.

CollectionDetailsAction - Class in org.intermine.web.struts

Action that creates a table of collection elements for display.

CollectionDetailsAction() - Constructor for class org.intermine.web.struts.CollectionDetailsAction

CollectionTableAction - Class in org.intermine.web.struts

Action that creates a table of collection elements for display in a table widget.

CollectionTableAction() - Constructor for class org.intermine.web.struts.CollectionTableAction

collectionToSQLString(Collection<? extends SQLStringable>, String) - Static method in class org.intermine.sql.query.Query

Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.

collectionToSQLString(Collection<? extends SQLStringable>, Collection<String>, String) - Static method in class org.intermine.sql.query.Query

Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.

CollectionUtil - Class in org.intermine.util

Utilities for Collections.

Column - Class in org.intermine.api.results

Configuration information for a column in a table

Column(Path, String, int, Class) - Constructor for class org.intermine.api.results.Column

Constructor that takes a Path object.

Column(Path, int, Class) - Constructor for class org.intermine.api.results.Column

Constructor that takes a Path object.

Column(String, int, Class) - Constructor for class org.intermine.api.results.Column

Constructor that takes a String name.

COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter

The key for the header columns

columnExists(Connection, String, String) - Static method in class org.intermine.sql.DatabaseUtil

Tests if a column exists in the database

columnFullNames - Variable in class org.intermine.web.logic.results.InlineResultsTable

ColumnHeaderStyle - Enum in org.intermine.webservice.server

Enumeration for outer join status.

columnId - Variable in class org.intermine.api.results.Column

combineBags() - Method in class org.intermine.api.bag.operations.BagOperation

combineBags() - Method in class org.intermine.api.bag.operations.RelativeComplement

CombinedIterator<E> - Class in org.intermine.util

An Iterator that combines the contents of various other Iterators.

CombinedIterator(List<Iterator<? extends E>>) - Constructor for class org.intermine.util.CombinedIterator

Constructs a CombinedIterator from a List of Iterators.

combineWith(ProfileMergeIssues) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues

Combine this set of merge issues with another set.

comment - Variable in class org.intermine.template.TemplateQuery

The private comment for this query.

commitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Request that the ObjectStore commits and closes the transaction, delegate to internal ObjectStoreWriter.

commitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Request that the ObjectStoreWriter commits and closes the transaction

commitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Request that the ObjectStoreWriter commits and closes the transaction

commitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Commits a transaction.

COMMON_KEYS - Static variable in class org.intermine.api.profile.UserPreferences

Common keys

CommutativeOperationInput - Class in org.intermine.webservice.server.lists

An input class for operations that are commutative.

CommutativeOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.CommutativeOperationInput

Constructor.

comparable(Class<?>, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint

Check whether the two arguments are of comparable types i.e. they are of similiar type and we know how to handle that type

compare(String, String) - Method in class org.intermine.api.bag.BagManager.ByTagOrder

compare(String, String) - Method in class org.intermine.api.bag.BagManager.CaseInsensitiveComparator

compare(InterMineObject, InterMineObject) - Method in class org.intermine.dataloader.SourcePriorityComparator

Compares two objects.

compare(Path, Path) - Method in class org.intermine.pathquery.PathLengthComparator

Compare paths by number elements they contain, shortest paths come first.

compare(AbstractTable, AbstractTable) - Method in class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator

Compare two AbstractTables using equalsIgnoreAlias().

compare(AbstractConstraint) - Method in class org.intermine.sql.query.AbstractConstraint

Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractConstraint

Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.

compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare the value of this AbstractValue with another.

compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constant

Compare this Constant to another AbstractValue.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constraint

Compare this Constraint with another AbstractConstraint, ignoring aliases in member fields and tables.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet

Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.

compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Field

Compare this field to another AbstractValue.

compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Function

Compare the value of this AbstractValue with another.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.InListConstraint

Compare this InListConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.NotConstraint

Compare this NotConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.

compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.OrderDescending

Compare the value of this AbstractValue with another.

compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.SubQueryConstraint

Compare this SubQueryConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.

compare(TemplateQuery, TemplateQuery) - Method in class org.intermine.template.TemplateComparator

Compare two TemplateQuery objects by title, falling back to name if the titles are identical.

compare(Object, Object) - Method in class org.intermine.util.NullFirstComparator

compare(Object, Object) - Method in class org.intermine.xml.full.RendererComparator

Compare two Class objects by name.

compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Compares 2 sets of AbstractConstraints

compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Compares 2 sets of AbstractConstraints

comparesActualToExpected() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

compareSelectLists(List<SelectValue>, List<SelectValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Compares two Lists of SelectValues, and returns true if all the items in the first List are present in the second List, ignoring the SelectValue alias.

compareTo(ParallelPrecomputer.Job) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer.Job

compareTo(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTable

Implements Comparable's method, so we can put PrecomputedTable objects into SortedMaps.

compareTo(Row) - Method in class org.intermine.sql.writebatch.Row

compareTo(SummaryPath) - Method in class org.intermine.web.logic.querybuilder.SummaryPath

compareTo(Item) - Method in class org.intermine.xml.full.Item

Compare items first by class, then by identifier, intended for creating ordered output files.

complete - Variable in class org.intermine.objectstore.query.ResultsInfo

complete - Variable in class org.intermine.sql.query.ExplainResult

completelyFalse(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Returns true if this constraint is always false, regardless of row values.

CompletelyFalseException - Exception in org.intermine.objectstore.intermine

Exception thrown if a Constraint is deemed to be completely false.

CompletelyFalseException() - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException

Constructor.

CompletelyFalseException(String) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException

Constructor.

CompletelyFalseException(Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException

Constructor.

CompletelyFalseException(String, Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException

Constructor.

completelyTrue(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Returns true if this constraint is always true, regardless of row values.

compose(F<B, C>) - Method in class org.intermine.webservice.server.core.F

Compose two functions f and g producing a function h such that h(x) = f(g(x)).

composeClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil

Return the Class for the array of Class objects.

composeClass(Set<Class<?>>) - Static method in class org.intermine.util.DynamicUtil

Return the Class for a set of Class objects.

composeDescriptiveClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil

Return the Class for the array of Class objects.

COMPUTE_TOTAL_COUNT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser

Compute total count parameter name.

con - Variable in class org.intermine.sql.logging.DatabaseWriter

con - Variable in class org.intermine.sql.precompute.BestQueryExplainer

con - Variable in class org.intermine.sql.query.NotConstraint

con - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

config - Variable in class org.intermine.web.displayer.ReportDisplayer

config - Variable in class org.intermine.web.logic.widget.Widget

ConfigAction - Class in org.intermine.bio.chado.config

A class that represents an action while processing synonyms, dbxrefs, etc.

ConfigAction() - Constructor for class org.intermine.bio.chado.config.ConfigAction

configAttr - Variable in class org.intermine.bio.dataconversion.GFF3Converter

configAttrClass - Variable in class org.intermine.bio.dataconversion.GFF3Converter

configExclude - Variable in class org.intermine.bio.dataconversion.GFF3Converter

configFileName - Variable in class org.intermine.task.SummariseObjectStoreTask

configTerm - Variable in class org.intermine.bio.dataconversion.GFF3Converter

ConfigurableMine - Interface in org.intermine.api.mines

A sub-interface of Mine to encapsulate the mutable elements of the interface, and not expose them the the consumer.

ConfigurableWebServiceServlet - Class in org.intermine.webservice.server.core

A servlet that can be configured entirely in XML.

ConfigurableWebServiceServlet() - Constructor for class org.intermine.webservice.server.core.ConfigurableWebServiceServlet

ConfigurationException - Exception in org.intermine.api.mines

An error caused when trying to configure something.

ConfigurationException(String) - Constructor for exception org.intermine.api.mines.ConfigurationException

Construct an exception with a message.

configure(Properties) - Method in interface org.intermine.api.mines.ConfigurableMine

Configure this mine with a the properties provided.

configure(Properties) - Method in class org.intermine.api.mines.HttpRequester

configure(Properties) - Method in class org.intermine.api.mines.LocalMine

configure(Properties) - Method in interface org.intermine.api.mines.MineRequester

Accept configuration provided in the form of properties.

configure(Properties) - Method in class org.intermine.api.mines.RemoteMine

configure(Properties) - Method in class org.intermine.sql.Database

Configures a datasource from a Properties object

configureDagTerm(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboParser

Configure dag terms with values from one entry.

configureDynamicAttributes(Object) - Method in class org.intermine.task.DynamicAttributeTask

Look at set methods on a target object and lookup values in project properties.

configureItem(String, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter

Set up attributes and references for the Item created from a DagTerm.

configureSynonymItem(OboTermSynonym, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter

Set up attributes and references for the Item created from a DagTermSynonym.

conn - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

conn - Variable in class org.intermine.sql.precompute.PrecomputedTableManager

connect() - Method in class org.intermine.webservice.client.util.HttpConnection

Opens connection.

connection - Variable in class org.intermine.api.tracker.TrackerDelegate

connection - Variable in class org.intermine.api.tracker.xml.TrackHandler

connectionTakenBy - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

connInUse - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

cons - Variable in class org.intermine.sql.query.ConstraintSet

ConsistentSet<E> - Class in org.intermine.util

A Set that allows for its member objects to be changed whilst still belonging to the set.

ConsistentSet() - Constructor for class org.intermine.util.ConsistentSet

Constructor.

Constant - Class in org.intermine.sql.query

A representation of a constant value in an SQL query.

Constant(String) - Constructor for class org.intermine.sql.query.Constant

Constructor for this Constant object.

constant(B) - Static method in class org.intermine.webservice.server.core.F

Construct a constant function that discards its input and always returns the same value.

Constants - Class in org.intermine.api.config

A single constant.

Constants - Class in org.intermine.bio.util

Constants - Class in org.intermine.web.logic

Container for ServletContext and Session attribute names used by the webapp

Constraint - Class in org.intermine.objectstore.query

Abstract reperesentation of a query constraint.

Constraint() - Constructor for class org.intermine.objectstore.query.Constraint

Constraint - Class in org.intermine.sql.query

A representation of a normal constraint, comparing two AbstractValue objects.

Constraint(AbstractValue, int, AbstractValue) - Constructor for class org.intermine.sql.query.Constraint

Constructor for a Constraint object.

constraintAttributes - Variable in class org.intermine.pathquery.PathQueryHandler

constraintCode - Variable in class org.intermine.pathquery.PathQueryHandler

constraintDescriptions - Variable in class org.intermine.template.TemplateQuery

Descriptions of constraints

ConstraintHelper - Class in org.intermine.objectstore.query

Static methods to create Lists of Constraint objects in a query and Constraints in a query relating to a given QueryClass, plus helper methods for dealing with Constraints.

ConstraintInput - Class in org.intermine.web.logic.template

Simple object that carries constraint values for other processing.

ConstraintInput(String, String, String, ConstraintOp, String, List<String>, String) - Constructor for class org.intermine.web.logic.template.ConstraintInput

ConstraintLoad constructor.

constraintLogic - Variable in class org.intermine.pathquery.PathQueryHandler

ConstraintOptions - Class in org.intermine.api.query.range

A bundle of options consumed by the AbstractHelper when generating constraint sets for a set of ranges.

ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp) - Constructor for class org.intermine.api.query.range.ConstraintOptions

Construct a new set of constraint options.

ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp, String, String) - Constructor for class org.intermine.api.query.range.ConstraintOptions

Construct a new set of constraint options.

constraintPath - Variable in class org.intermine.pathquery.PathQueryHandler

constraints - Variable in class org.intermine.objectstore.query.ConstraintSet

Constraints - Class in org.intermine.pathquery

Builds constraints for the PathQuery.

ConstraintSet - Class in org.intermine.objectstore.query

Groups a series of Constraints together.

ConstraintSet(ConstraintOp) - Constructor for class org.intermine.objectstore.query.ConstraintSet

Construct empty ConstraintSet

ConstraintSet - Class in org.intermine.sql.query

A representation of a set of constraints ORed together.

ConstraintSet() - Constructor for class org.intermine.sql.query.ConstraintSet

Constructor for a ConstraintSet object.

constraintSetToString(SqlGenerator.State, StringBuffer, ConstraintSet, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a ConstraintSet object into a String suitable for putting in an SQL query.

constraintSwitchOffAbility - Variable in class org.intermine.template.TemplateQuery

Configuration for switch-off-ability of constraints

constraintToString(SqlGenerator.State, StringBuffer, Constraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a Constraint object into a String suitable for putting in an SQL query.

constraintToString(Query, Constraint, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts a Constraint into a String.

ConstraintTraverseAction - Interface in org.intermine.objectstore.query

ConstraintTraverseActions are passed to the traverseConstraints() method.

ConstraintValueParser - Class in org.intermine.pathquery

Parser for parsing constraint value.

constraintValues - Variable in class org.intermine.pathquery.PathQueryHandler

ConstraintWithBag - Interface in org.intermine.objectstore.query

Common interface for BagConstraint and MultipleInBagConstraint defining the getBag() method.

constructQueries(boolean, ObjectStore, String, String) - Static method in class org.intermine.task.PrecomputeTask

Create queries for given path.

constructQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Construct an objectstore query represented by the given path.

ContactAction - Class in org.intermine.web.struts

Action handles submission of user feedback form.

ContactAction() - Constructor for class org.intermine.web.struts.ContactAction

ContactForm - Class in org.intermine.web.struts

Form bean representing feedback form.

ContactForm() - Constructor for class org.intermine.web.struts.ContactForm

Creates a new instance of ContactForm

contains(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to contain a value.

contains(Object) - Method in class org.intermine.util.AlwaysSet

contains(int) - Method in class org.intermine.util.IntPresentSet

Returns whether the given int is present in this set.

contains(Integer) - Method in class org.intermine.util.IntPresentSet

Returns whether the given Integer is present in this set.

contains(Collection<?>, Object) - Static method in class org.intermine.web.logic.WebUtil

So we can test set membership in JSPs.

contains(Object) - Method in class org.intermine.webservice.client.lists.ItemList

contains(Object) - Method in class org.intermine.webservice.client.results.ResultRowList

contains(ItemList, Item...) - Method in class org.intermine.webservice.client.services.ListService

Report whether the given list contains all the items in the supplied array.

containsAll(Collection<?>) - Method in class org.intermine.util.AlwaysSet

containsAll(Collection<?>) - Method in class org.intermine.util.PseudoSet

containsAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList

containsAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList

containsCollections() - Method in class org.intermine.pathquery.Path

Return true if and only if any part of the path is a collection.

ContainsConstraint - Class in org.intermine.objectstore.query

Constrain whether a QueryClass is member of a QueryReference or not.

ContainsConstraint(QueryReference, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ContainsConstraint

Constructor for ContainsConstraint.

ContainsConstraint(QueryReference, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ContainsConstraint

Constructor for ContainsConstraint.

ContainsConstraint(QueryReference, ConstraintOp) - Constructor for class org.intermine.objectstore.query.ContainsConstraint

Constructor for ContainsConstraint, constrain a reference/collection to be NULL/ NOT NULL

containsConstraintToString(SqlGenerator.State, StringBuffer, ContainsConstraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a ContainsConstraint object into a String suitable for putting in an SQL query.

containsHeaders(String, StringBuffer) - Method in class org.intermine.web.struts.ContactForm

Check part of the message for injected headers.

containsKey(Object) - Method in class org.intermine.util.AlwaysMap

containsKey(Object) - Method in class org.intermine.util.IdentityMap

containsKey(Object) - Method in class org.intermine.util.ReferenceMap

containsKey(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory

Always returns true because get always returns an Object.

containsKey(Map<?, ?>, Object) - Static method in class org.intermine.web.logic.WebUtil

So we can test map membership in JSPs.

containsReferences() - Method in class org.intermine.pathquery.Path

Return true if and only if any part of the path is a reference.

containsValue(Object) - Method in class org.intermine.util.AlwaysMap

containsValue(Object) - Method in class org.intermine.util.IdentityMap

containsValue(Object) - Method in class org.intermine.util.ReferenceMap

ContentType - Enum in org.intermine.api.mines

An enumeration of the content-types we know about.

ContentType - Class in org.intermine.webservice.client.core

Simple class wrapping content type information.

ContextNotInitialisedException - Exception in org.intermine.web.context

An error thrown when the InterMineContext object has not been initialised.

ContextNotInitialisedException(String) - Constructor for exception org.intermine.web.context.ContextNotInitialisedException

convert(ResultSet, Query, ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter

Method to convert from SQL results to InterMine object-based results.

convert(List<ResultElement>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ResultElementConverter

Converts data from ResultElement to Objects.

convert(Item) - Static method in class org.intermine.xml.full.ItemHelper

Convert an XML item to a data model one

convert(ReferenceList) - Static method in class org.intermine.xml.full.ItemHelper

Convert a xml ReferenceList to a fulldata ReferenceList that can then be stored with ItemWriter

convert(Reference) - Static method in class org.intermine.xml.full.ItemHelper

Convert a xml Reference to a fulldata Reference that can then be stored with ItemWriter

convert(Attribute) - Static method in class org.intermine.xml.full.ItemHelper

Convert a xml Attribute to a fulldata Attribute that can then be stored with ItemWriter

convert(Item) - Static method in class org.intermine.xml.full.ItemHelper

Convert a data model item to an XML one

ConvertBagController - Class in org.intermine.web.struts

ConvertBagController() - Constructor for class org.intermine.web.struts.ConvertBagController

ConvertedObjectPair - Class in org.intermine.api.bag

A class to represent the mapping between an object before type conversion and the converted object.

ConvertedObjectPair(InterMineObject, InterMineObject) - Constructor for class org.intermine.api.bag.ConvertedObjectPair

Create a new ConvertedObjectPair.

converter - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

converter - Variable in class org.intermine.bio.task.GFF3ConverterTask

ConverterTask - Class in org.intermine.task

Task superclass for invoking converters.

ConverterTask() - Constructor for class org.intermine.task.ConverterTask

convertToClasses(Set<String>) - Static method in class org.intermine.util.DynamicUtil

Convert a set of interface names to a set of Class objects

copyField(FastPathObject, FastPathObject, Source, Source, FieldDescriptor, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Copies the value of the field given from the source object into the destination object.

copyInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil

Create a copy of given InterMineObject with *no* id set and copies of collections

correction - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

CorrectionCoefficient - Interface in org.intermine.web.logic.widget

An Interface which defines when/how a correction coefficient can be applied to the results obtained by a enrichment widget

correctOfficialName(String, String) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Unify variations on similar official names.

count(PathQuery) - Method in class org.intermine.api.query.QueryExecutor

Take a query and return the results row count.

count - Variable in class org.intermine.dataconversion.FullXmlConverter

count(Query, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Counts the number of rows the query will produce

count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Counts the number of rows the query will produce

count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Counts the number of rows the query will produce

count(Query, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore

Counts the number of rows the query will produce

count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Counts the number of rows the query will produce

COUNT - Static variable in class org.intermine.objectstore.query.QueryFunction

Count rows

count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Counts the number of rows the query will produce

count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Counts the number of rows the query will produce

COUNT - Static variable in class org.intermine.sql.query.Function

COUNT(*) aggregate function - takes no operands.

CountProcessor - Class in org.intermine.webservice.server.core

A class that processes counts.

CountProcessor() - Constructor for class org.intermine.webservice.server.core.CountProcessor

Constructor

countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.DoNothingIdResolver

countResolutions(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Return the count of matching primary identifiers for a particular identifier

countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Return the count of matching primary identifiers for a particular identifier

CountTableController - Class in org.intermine.web.struts

Start a count in a separate thread of the number of rows in the PagedTable given by the "resultsTable" request attribute.

CountTableController() - Constructor for class org.intermine.web.struts.CountTableController

countWithConnection(Connection, Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Counts the results in a query, given a Connection.

create() - Method in class org.intermine.bio.postprocess.CreateLocationOverlapIndex

Create an int4range or bioseg index on the start and end columns of the of the location table.

create(Class<? extends FastPathObject>, Class<?>[]) - Static method in class org.intermine.util.DynamicBean

Create a DynamicBean

CREATE_SYNONYM_ACTION - Static variable in class org.intermine.bio.dataconversion.SequenceProcessor

An action that makes a synonym.

CreateAccountAction - Class in org.intermine.web.struts

CreateAccountAction() - Constructor for class org.intermine.web.struts.CreateAccountAction

CreateAccountForm - Class in org.intermine.web.struts

Form bean to represent the inputs to create a new user account

CreateAccountForm() - Constructor for class org.intermine.web.struts.CreateAccountForm

createAllelesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Create a temporary table of allele feature_ids.

createAnonymousProfile() - Method in class org.intermine.api.profile.ProfileManager

Create a profile not tied to an entry in the user db.

createAttributePath(String[], int) - Method in class org.intermine.web.logic.widget.WidgetLdr

Return the path of the attribute at the the position index in the paths given in input without reference to subclass.

createBag(String, String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.Profile

Create a bag and save it to the userprofile database.

createBag(String, String, String, Map) - Method in class org.intermine.api.util.AnonProfile

createBagFromPathQuery(PathQuery, String, String, String, Profile, InterMineAPI) - Static method in class org.intermine.web.logic.bag.BagHelper

Create a bag for the given profile and bag name from a PathQuery.

createBagTable(Database, Connection, String, Collection<?>, Class<?>) - Static method in class org.intermine.sql.DatabaseUtil

Create a new table the holds the contents of the given Collection (bag).

createBagValuesTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil

Create the table 'bagvalues' containing the values of the key field objects contained in a bag and an extra values

createBasicLocalProfile(String, String, String) - Method in class org.intermine.api.profile.ProfileManager

Create a new Profile with the given username, password and api-key.

createClassFindingQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Takes a String representation of a query (a path), and creates a query.

createClob() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Creates a new empty Clob that is valid for this ObjectStore.

createClob() - Method in interface org.intermine.objectstore.ObjectStore

Creates a new empty Clob that is valid for this ObjectStore.

createClob() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Creates a new empty Clob that is valid for this ObjectStore.

createClob() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Creates a new empty Clob that is valid for this ObjectStore.

CreateCollectionAction - Class in org.intermine.bio.chado.config

An action that creates a collection of objects from value.

CreateCollectionAction(String, String, String, boolean) - Constructor for class org.intermine.bio.chado.config.CreateCollectionAction

Create a new CreateCollectionAction object.

createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.AbstractHelper

Extending classes may with to override this method if they need to adjust the main constraint set in some way, such as adding an extra constraint.

createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.IntHelper

createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.StringHelper

createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in interface org.intermine.api.query.RangeHelper

createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.bio.query.range.ChromosomeLocationHelper

createConstraintStructure(LogicExpression, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper

Given a LogicExpression, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.

createConstraintStructure(LogicExpression.Node, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper

Given a LogicExpression.Node, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.

createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

Create a new CrossReference.

createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Create a new CrossReference.

createDefaultBagQuery(String, BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, Collection<String>) - Static method in class org.intermine.api.bag.BagQueryHelper

Create a BagQuery that constrains the class key fields of the given type.

createDefaultFeedbackMsg(HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm

Create the default feedback messages.

createFeatureTempTable(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Create a temporary table containing only the features that interest us.

createFlankingFeatures() - Method in class org.intermine.bio.postprocess.CreateFlankingRegions

Iterate over genes in database and create flanking regions.

CreateFlankingRegions - Class in org.intermine.bio.postprocess

Create features to represent flanking regions of configurable distance either side of gene features.

CreateFlankingRegions(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateFlankingRegions

Create a new CreateFlankingRegions object that will operate on the given ObjectStoreWriter.

createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

createFromDb(Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Read IdResolver contents from a database.

createFromDb(String, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Read IdResolver contents from a database.

createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Read IdResolver contents from a database.

createFromDb(Database) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

createFromDb(Database) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

createFromFile(File) - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File, Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File) - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File) - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File) - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File) - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory

Populate the ID resolver from a tab delimited file

createFromFile(File) - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory

Populate the ID resolver from a tab delimited file

createFromWb2NcbiFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

Populate the ID resolver from a tab delimited file

createFromWormIdFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

Populate the ID resolver from a tab delimited file

createGetRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service

Creates GET request.

createIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory

createIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Build an IdResolver from Entrez Gene gene_info file

createIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Build an IdResolver from Entrez Gene gene_info file.

createIdResolver() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Build an IdResolver for FlyBase by accessing a FlyBase chado database.

createIdResolver() - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory

Build an IdResolver for HGNC.

createIdResolver() - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Create and IdResolver from source information.

createIdResolver() - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

Build an IdResolver.

createIdResolver() - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory

createIdResolver() - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

Build an IdResolver for WormBase by accessing a WormBase chado database.

createIdResolver() - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory

Build an IdResolver from Entrez Gene gene_info file

createIndex(Connection, String, IndexStatement, int) - Method in class org.intermine.task.CreateIndexesTask

Create an named index on the specified columns of a table.

CreateIndexesTask - Class in org.intermine.task

Task to create indexes on a database holding objects conforming to a given model by reading that model's primary key configuration information.

CreateIndexesTask() - Constructor for class org.intermine.task.CreateIndexesTask

createInsertionTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Create a temporary table from pairs of insertions (eg.

createIntergenicRegionFeatures() - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil

Create IntergenicRegion objects

createIntergenicRegionFeatures(Set<Location>, Map<Integer, Set<Gene>>, Integer) - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil

Return an iterator over a Set of IntergenicRegion objects that don't overlap the Locations in the locationSet argument.

createIntronFeatures() - Method in class org.intermine.bio.postprocess.IntronUtil

Create Intron objects

createIntronFeatures(Set<Location>, SequenceFeature, Location, Gene) - Method in class org.intermine.bio.postprocess.IntronUtil

Return a set of Intron objects that don't overlap the Locations in the locationSet argument.

createIsoformEntry(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

no: features gene items, just identifiers - for memory reasons sequence, length, molecular weight, md5checksum components - per rachel isoforms - per mike

createItem(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler

Create the sequence item from the converter.

createItem(String) - Method in class org.intermine.dataconversion.DataConverter

Create item for the given class name.

createKeyStore() - Method in class org.intermine.web.task.KeyStoreTask

Create and return the configured key-store.

createList(Query) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Converts a constraint from a query into a List of Constraint objects.

createList(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Return a List of Constraint objects that relate to the given FromElement.

createList(ListService.ListCreationInfo) - Method in class org.intermine.webservice.client.services.ListService

Create a new list on the server by specifying its content.

createLocatedGenesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Create a temporary table containing the ids of the located genes.

CreateLocationOverlapIndex - Class in org.intermine.bio.postprocess

Create an index on the location table to be used for range queries.

CreateLocationOverlapIndex(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateLocationOverlapIndex

Construct a new CreateLocationRange

createLocations(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return true if Location objects should be made for all features (which is the default).

createNewProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager

Create a new profile in db with username and password given in input

createObject(String) - Method in class org.intermine.dataloader.DirectDataLoader

Create a new object of the given class name and give it a unique ID.

createObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader

Create a new object of the given class and give it a unique ID.

createObject(Set<? extends Class<?>>) - Static method in class org.intermine.util.DynamicUtil

Create a DynamicBean from a Set of Class objects

createObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil

Create a new object given a class (not an interface).

createObjectStoreBag() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Returns a new empty ObjectStoreBag for this ObjectStore, delegate to internal ObjectStoreWriter.

createObjectStoreBag() - Method in interface org.intermine.objectstore.ObjectStore

Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.

createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Creates a new empty ObjectStoreBag object that is valid for this ObjectStore.

createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.

createOverlapRelations(List<String>, boolean) - Method in class org.intermine.bio.postprocess.CalculateLocations

Deprecated.

You should be using the create-overlap-view task instead

createOverlaps(ObjectStore, SequenceFeature, List<?>, boolean, ObjectStoreWriter, Map<String, Integer>) - Static method in class org.intermine.bio.postprocess.OverlapUtil

Creates OverlapRelations for overlapping SequenceFeature objects that are located on the given subject (generally a Chromosome).

createPasswordChangeToken(String) - Method in class org.intermine.api.profile.ProfileManager

Creates a password change token assigned to the given username that will expire after a day.

createPathConstraint(PathConstraint, String) - Method in class org.intermine.api.profile.PathQueryUpdate

Create a pathconstraint with the same operator and value of path contraint given in input and with the path given in input

createPathQuery() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.

createPathQuery(String) - Method in class org.intermine.webservice.client.services.QueryService

Constructs a PathQuery from its XML representation.

createPathQueryView(ObjectStore, WidgetConfig) - Method in class org.intermine.web.logic.widget.Widget

Create a pathquery having a view composed by all items set in the view attribute in the config file

createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.

createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher

Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.

createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.HintingFetcher

Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.

createPKQuery(InterMineObject, Source, boolean) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.

createPKQuery(InterMineObject, Source, boolean) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher

Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.

createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Adds a Query to handle a primary key to a Set.

createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.HintingFetcher

Adds a Query to handle a primary key to a Set.

createPostRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service

Creates POST request.

createProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager

Creates a profile in the userprofile database.

createProfileWithoutBags(Profile) - Method in class org.intermine.api.profile.ProfileManager

Creates a profile in the userprofile database without adding bag.

createQueryFieldByPath(String, Query, boolean) - Method in class org.intermine.web.logic.widget.WidgetLdr

Create a queryField starting from the path given in input and add the contain constraints between all the queryclass composing the path.

createQueryForExampleObject(Model, InterMineObject, Set<String>) - Static method in class org.intermine.objectstore.query.QueryCreator

Generates a query that searches for all objects in the database that have the fieldnames set to the values in the object.

createQueryForId(Integer, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator

Create a query that will retrieve an object from the objectstore, given an ID.

createQueryForIds(Collection<Integer>, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator

Create a query that will retrieve all objects with the given IDs from the objectstore.

createQueryForQueryNodeValues(Query, QueryNode) - Static method in class org.intermine.objectstore.query.QueryCreator

Create a query that will list the options for a particular field or class in a query, given the existing constraints For example: Original query: SELECT c, d FROM Company AS c, Department AS d WHERE c.departments CONTAINS d AND c.name LIKE 'A%' We want to know the possible department names are that we might want to constrain Returned query: SELECT DISTINCT d.name FROM Company AS c, Department AS d WHERE c.departments CONTAINS d AND c.name LIKE 'A%'

createRAMIndex(String) - Method in class org.intermine.web.autocompletion.AutoCompleter

create the RAMIndex for the search engine

CreateReferences - Class in org.intermine.bio.postprocess

Fill in additional references/collections in genomic model

CreateReferences(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateReferences

Construct with an ObjectStoreWriter, read and write from same ObjectStore

CreateSearchIndexTask - Class in org.intermine.web.task

Create a the Lucene keyword search index for a mine.

CreateSearchIndexTask() - Constructor for class org.intermine.web.task.CreateSearchIndexTask

createSignature() - Method in enum org.intermine.webservice.server.JWTBuilder.Algorithm

createSimpleObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader

Create a 'simple object' which doesn't inherit from InterMineObject and doesn't have an id.

createSingletons() - Method in class org.intermine.bio.chado.config.CreateCollectionAction

If true, create only one object of class className with each possible fieldName; if false, multiple objects with the same value for fieldName might be created

createSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

createSpanningLocations(String, String, String) - Method in class org.intermine.bio.postprocess.CalculateLocations

Create a Location that spans the locations of some child objects.

createSQLStatement(String, String) - Method in class org.intermine.sql.logging.DatabaseWriter

Creates an SQL String suitable for initialising a PreparedStatement

createSubFeatureIdTempTable(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Create a temporary table of all feature_ids for a given submission.

createSuperUser(String, String, String) - Method in class org.intermine.api.profile.ProfileManager

Create a super-user with the given username, password and API-key.

createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Create a new Synonym.

createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

Create a new Synonym.

createSynonym(Item, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Create a new Synonym.

createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Create a new Synonym.

createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've created it.

createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've created it.

CreateSynonymAction - Class in org.intermine.bio.chado.config

An action that sets a Synonym.

CreateSynonymAction() - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction

Make a synonym

CreateSynonymAction(Pattern) - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction

Make a synonym and use the type from chado ("symbol", "identifier" etc.) as the Synonym type.

createTempBagTable(ConstraintWithBag) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates a temporary bag table for the given BagConstraint.

createTempBagTable(Connection, ConstraintWithBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates a temporary bag table for the given BagConstraint.

createTempBagTable(Connection, QueryClassBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates a temporary bag table for the given QueryClassBag.

createTempBagTables(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Create temporary tables for use with Query that use bags.

CreateTemplateAction - Class in org.intermine.web.struts

Action to create a new TemplateQuery from current query.

CreateTemplateAction() - Constructor for class org.intermine.web.struts.CreateTemplateAction

createToken(Profile, int) - Method in class org.intermine.webservice.server.user.DeletionTokens

Create a new DeletionToken

createTrackerTable(Connection) - Method in class org.intermine.api.tracker.AbstractTracker

Create the table where the tracker saves data

createTrackerTable(Connection) - Method in interface org.intermine.api.tracker.Tracker

Create the table where the tracker saves data

createTrailLabel(InterMineObject, Model) - Static method in class org.intermine.web.struts.ObjectTrailController

Create trail element label.

createUtrRefs() - Method in class org.intermine.bio.postprocess.CreateReferences

Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the corresponding UTRs.

createView() - Method in class org.intermine.bio.postprocess.OverlapViewTask

Drop the sequencefeatureoverlappingfeatures table and replace it with a view that uses the bioseg type to calculate the overlaps.

createWithObjects(String, Item, String, String) - Method in class org.intermine.bio.dataconversion.GoConverter

Given the 'with' text from a gene_association entry parse for recognised identifier types and create Gene or Protein items accordingly.

CreationEvent - Class in org.intermine.api.search

A representation of a notification a web searchable object has been created.

CreationEvent(WebSearchable) - Constructor for class org.intermine.api.search.CreationEvent

Constructor.

CSVExportForm - Class in org.intermine.web.struts

A form to hold options for CSV and tab separated output.

CSVExportForm() - Constructor for class org.intermine.web.struts.CSVExportForm

CSVFormatter - Class in org.intermine.webservice.server.output

Formats data to comma separated data format.

CSVFormatter() - Constructor for class org.intermine.webservice.server.output.CSVFormatter

Construct a CSV formatter.

CSVHttpExporter - Class in org.intermine.web.logic.export.http

Exporter that exports table with results in comma separated format.

CSVHttpExporter() - Constructor for class org.intermine.web.logic.export.http.CSVHttpExporter

Constructor.

CSVRowFormatter - Class in org.intermine.web.logic.export.rowformatters

Row formatter formats line as comma separated strings.

CSVRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.CSVRowFormatter

Constructor.

currentArray - Variable in class org.intermine.webservice.server.output.JSONResultsIterator

currentIterator - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

currentIterator - Variable in class org.intermine.util.CombinedIterator

currentMap - Variable in class org.intermine.webservice.server.output.JSONResultsIterator

currentNodePath - Variable in class org.intermine.pathquery.PathQueryHandler

CurrentQueryAction - Class in org.intermine.web.struts

Action to display the query builder (if there is a current query) or redirect to project.sitePrefix.

CurrentQueryAction() - Constructor for class org.intermine.web.struts.CurrentQueryAction

CustomOAuthProvider - Class in org.intermine.web.struts.oauth2

A representation of an OAuth provider which has been configured entirely in web-properties.

CustomOAuthProvider(Properties, String) - Constructor for class org.intermine.web.struts.oauth2.CustomOAuthProvider

Construct a new provider.

CustomPrintWriter - Class in org.intermine.web.logic.export

Customized PrintWriter that terminates end of the lines with defined line separator.

CustomPrintWriter(OutputStream, String) - Constructor for class org.intermine.web.logic.export.CustomPrintWriter

Constructor.

D

dagFilename - Variable in class org.intermine.bio.dataconversion.OboConverter

Database - Class in org.intermine.sql

Class that represents a physical SQL database

Database() - Constructor for class org.intermine.sql.Database

No argument constructor for testing purposes

Database(Properties) - Constructor for class org.intermine.sql.Database

Constructs a Database object from a set of properties

database - Variable in class org.intermine.sql.precompute.PrecomputedTableManager

database - Variable in class org.intermine.task.AnalyseDbTask

database - Variable in class org.intermine.task.BuildDbTask

database - Variable in class org.intermine.task.GrantTask

database - Variable in class org.intermine.task.RetrieveMetadataTask

database - Variable in class org.intermine.task.StoreMetadataTask

databaseAlias - Variable in class org.intermine.task.BuildDbTask

databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.

databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.

DatabaseConnectionException - Exception in org.intermine.sql

Exception thrown on failing to object a database connection.

DatabaseConnectionException() - Constructor for exception org.intermine.sql.DatabaseConnectionException

Constructs an DatabaseConnectionException

DatabaseConnectionException(String) - Constructor for exception org.intermine.sql.DatabaseConnectionException

Constructs an ObjectStoreException with the specified detail message.

DatabaseConnectionException(Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException

Constructs an ObjectStoreException with the specified nested throwable.

DatabaseConnectionException(String, Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException

Constructs an ObjectStoreException with the specified detail message and nested throwable.

databaseEmpty() - Method in class org.intermine.dataloader.EquivalentObjectHints

Returns true if the database was empty at the start of the run.

DatabaseFactory - Class in org.intermine.sql

Creates Databases

databases - Static variable in class org.intermine.sql.DatabaseFactory

DatabaseSchema - Class in org.intermine.objectstore.intermine

An object that represents the mapping of a Model onto a relational database.

DatabaseSchema(Model, List<ClassDescriptor>, boolean, Set<String>, int, boolean, boolean) - Constructor for class org.intermine.objectstore.intermine.DatabaseSchema

Returns an instance of DatabaseSchema, for the given Model and and List of truncated classes.

DatabaseSchema.Fields - Class in org.intermine.objectstore.intermine

Inner class to hold information on Attributes and References.

DatabaseUtil - Class in org.intermine.sql

Collection of commonly used Database utilities

DatabaseUtil.Type - Enum in org.intermine.sql

DatabaseWriter - Class in org.intermine.sql.logging

Writes tab-separated Strings to a database table

DatabaseWriter() - Constructor for class org.intermine.sql.logging.DatabaseWriter

Construct an empty DatabaseWriter for testing purposes

DatabaseWriter(Connection, String) - Constructor for class org.intermine.sql.logging.DatabaseWriter

Construct a DatabaseWriter

DataChangedException - Exception in org.intermine.objectstore

An Exception that may be thrown by an ObjectStore indicating that a request cannot be serviced because the database has changed since the request was started.

DataChangedException() - Constructor for exception org.intermine.objectstore.DataChangedException

Constructs an DataChangedException

DataChangedException(String) - Constructor for exception org.intermine.objectstore.DataChangedException

Constructs an DataChangedException with the specified detail message.

DataChangedException(Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException

Constructs an DataChangedException with the specified nested throwable.

DataChangedException(String, Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException

Constructs an DataChangedException with the specified detail message and nested throwable.

DataConverter - Class in org.intermine.dataconversion

Abstract parent class of all DataConverters

DataConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DataConverter

Constructor that should be called by children

DataConverterStoreHook - Interface in org.intermine.dataconversion

A hook that is called immediately before each Item is stored by the DataConverter.

dataDir - Variable in class org.intermine.task.DirectoryConverterTask

DataLoader - Class in org.intermine.dataloader

Loads information from a data source into the InterMine database.

DataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.DataLoader

Construct a DataLoader

DataLoaderHelper - Class in org.intermine.dataloader

Class providing utility methods to help with primary key and data source priority configuration

DataService - Class in org.intermine.webservice.server.data

DataService(InterMineAPI) - Constructor for class org.intermine.webservice.server.data.DataService

DataSetLdr - Interface in org.intermine.web.logic.widget

An Interface which defines a frame in which data can be retrieved, organised and created to then be passed to a JFreeChart for representation

datasource - Variable in class org.intermine.sql.Database

dataTracker - Variable in class org.intermine.dataloader.BatchingFetcher

DataTracker - Class in org.intermine.dataloader

Interface providing access to data tracking.

DataTracker(Database, int, int) - Constructor for class org.intermine.dataloader.DataTracker

Constructor for DataTracker.

dataTracker - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

DATE_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint

db - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

DBConverter - Class in org.intermine.dataconversion

A DataConverter that reads from a Database and writes to a ItemWriter

DBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.dataconversion.DBConverter

Constructor

DBConverterTask - Class in org.intermine.task

Task to call DBConverters.

DBConverterTask() - Constructor for class org.intermine.task.DBConverterTask

dbIdsStored - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Produce an entry in the DB log.

dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Produce an entry in the DB log.

declarePrinted() - Method in class org.intermine.webservice.server.output.JSONFormatter

Signal that we have started printing results and that it isn't safe to print headers.

decode(String) - Method in class org.intermine.web.security.Base64PublicKeyDecoder

decode(String) - Method in interface org.intermine.web.security.KeyDecoder

Decode the string and make the key.

decodeDbDescription(ObjectStore, String) - Static method in class org.intermine.objectstore.query.ClobAccess

Decodes a String from the database representing a clob object.

decodeLZWString(String) - Static method in class org.intermine.webservice.server.query.QueryRequestParser

Take in a LZW encoded string and return a decoded plain-text string.

DecodingException - Exception in org.intermine.web.security

The error that indicates we cannot decode something.

DecodingException(Throwable) - Constructor for exception org.intermine.web.security.DecodingException

Constructor.

decomposePath() - Method in class org.intermine.pathquery.Path

Returns a list of paths, each corresponding to one step further along the path.

decompressLZW(List<Integer>) - Static method in class org.intermine.webservice.server.query.QueryRequestParser

Decompress a list of output ks to a string.

DEFAULT - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext

The default context - normal operation with no time limit.

DEFAULT - Static variable in class org.intermine.webservice.client.results.Page

The default page size (from the beginning to the maximum page size)

DEFAULT_ALGORITHM - Static variable in class org.intermine.web.security.KeySigner

The default algorithm to use

DEFAULT_BATCH_SIZE - Static variable in class org.intermine.api.query.PathQueryExecutor

default batch size

DEFAULT_BATCH_SIZE - Static variable in class org.intermine.objectstore.query.ResultsBatches

This is the default batch size for Results objects

DEFAULT_CALLBACK - Static variable in class org.intermine.webservice.server.WebService

Default jsonp callback

DEFAULT_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

10 000 000 default size actually means that web service will return all results

DEFAULT_MAX_VALUES - Static variable in class org.intermine.objectstore.ObjectStoreSummary

The default number of values to make available for UI dropdowns - attributes with more values will not become dropdowns.

DEFAULT_MESSAGE - Static variable in class org.intermine.api.bag.BagQueryHelper

Message associated with default bag query.

DEFAULT_OPERATOR - Static variable in class org.intermine.web.logic.Constants

Session attribut containing the default operator name, either 'and' or 'or'.

DEFAULT_RESULT_SIZE - Static variable in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Default value of size parameter

DEFAULT_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants

Default size of table implemented by PagedTable.

defaultClsCol - Variable in class org.intermine.bio.dataconversion.IdResolverFactory

defaultName - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

defaultNS - Variable in class org.intermine.bio.ontology.OboParser

Default namespace.

DefaultOAuthProvider - Class in org.intermine.web.struts.oauth2

A representation of an OAuth provider which is one of the default providers provided for end-users.

DefaultOAuthProvider(Properties, OAuthProviderType) - Constructor for class org.intermine.web.struts.oauth2.DefaultOAuthProvider

Construct a new provider.

defaultSymbol - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

DelegatedIdentity - Class in org.intermine.web.struts.oauth2

A simple struct class for containing information about a delegated identity.

DelegatedIdentity(String, String, String, String) - Constructor for class org.intermine.web.struts.oauth2.DelegatedIdentity

Construct a new delegated identity.

delete() - Method in class org.intermine.api.bag.SharingInvite

delete() - Method in class org.intermine.api.profile.InterMineBag

Delete this bag from the userprofile database, bag should not be used after this method has been called.

delete() - Method in class org.intermine.api.profile.InvalidBag

Delete this bag from the userprofile database, bag should not be used after this method has been called.

DELETE - Static variable in class org.intermine.api.profile.ModelUpdate

label in modelUpdate.properties file to identify deleted classes or fields

delete() - Method in class org.intermine.api.profile.StorableBag

Delete this bag.

delete(InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Delete an object from this ObjectStore, delegate to internal ObjectStoreWriter.

delete(QueryClass, Constraint) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Deletes a set of objects from this ObjectStore.

delete(InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Delete an object from this ObjectStore

delete(QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Deletes a set of objects from this ObjectStore.

delete(InterMineObject) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Delete an object from this ObjectStore

delete(QueryClass, Constraint) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Deletes a set of objects from this ObjectStore.

delete(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Delete a precomputed table from the underlying database.

delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction

Delete some queries

delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction

Delete some templates.

delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UserTemplateAction

Delete a template query.

delete() - Method in class org.intermine.webservice.client.lists.ItemList

Call for this list to be deleted on the server.

deleteAllBagValues() - Method in class org.intermine.api.profile.InterMineBag

deleteAllBagValues() - Method in class org.intermine.api.profile.StorableBag

Remove all the values from the bag-value table.

deleteAllPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager

deleteApiKey(String) - Method in class org.intermine.dwr.AjaxServices

Delete a user's API key, thus disabling webservice access.

deleteBag(String) - Method in class org.intermine.api.profile.Profile

Delete a bag from the user account, if user is logged in also deletes from the userprofile database.

deleteBags() - Method in class org.intermine.api.profile.ModelUpdate

Delete all bags having as a type one of the classes deleted

deleteBagValues(List<String>) - Method in class org.intermine.api.profile.InterMineBag

Delete a given set of bag values from the bag value table.

deleteBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

deleteFrom(FromElement) - Method in class org.intermine.objectstore.query.Query

Remove a FromElement from the FROM clause

deleteFromGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query

Remove a QueryNode from the GROUP BY clause

deleteFromOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query

Remove a QueryOrderable from the ORDER BY clause

deleteFromSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query

Remove a QuerySelectable from the SELECT clause

deleteGlobalRepository(Profile) - Method in class org.intermine.api.search.GlobalRepository

deleteHistory(String) - Method in class org.intermine.api.profile.Profile

Remove an item from the query history.

deleteIndexDirectory() - Static method in class org.intermine.api.lucene.KeywordSearch

delete the directory used for the index (used in postprocessing)

deleteLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager

Delete a large object from the database based on a given metadata key.

deleteList(ItemList) - Method in class org.intermine.webservice.client.services.ListService

Deletes a list on the server.

deleteObjectTags(String, String, String) - Method in class org.intermine.api.profile.TagManager

Deletes all tags assigned to a specified object.

deletePreference(Profile, String) - Method in class org.intermine.api.profile.PreferencesManager

DeletePreferencesService - Class in org.intermine.webservice.server.user

A service that deletes a user's preferences.

DeletePreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeletePreferencesService

deleteProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager

Completely remove a profile and all of its associated data from the data-store.

deleteQuery(String) - Method in class org.intermine.api.profile.Profile

Delete a query

deleteRow(Connection, String, String, Object) - Method in class org.intermine.sql.writebatch.Batch

Deletes a row from the batch for a given table.

deleteRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch

Deletes a row from the batch for a given indirection table.

deleteRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Deletes a row from the batch.

deleteRow(String, Object) - Method in class org.intermine.sql.writebatch.TableBatch

Deletes a row from the batch.

deleteSomeBagValues(List<String>) - Method in class org.intermine.api.profile.StorableBag

Delete a given set of bag values from the bag value table.

deleteTableFromDatabase(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Delete a PrecomputedTable from the database.

deleteTag(Tag) - Method in class org.intermine.api.profile.TagManager

Delete a tag object from the database.

deleteTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager

Delete a tag by name from a web-searchable object.

deleteTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager

Delete a tag by name from a class-descriptor.

deleteTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager

Delete a tag by name from a reference-descriptor.

deleteTag(String, String, String, String) - Method in class org.intermine.api.profile.TagManager

Deletes a tag object from the database.

deleteTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices

Deletes tag.

deleteTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager

Deletes tags object from the database.

deleteTemplate(String, TrackerDelegate, boolean) - Method in class org.intermine.api.profile.Profile

Delete a template and its tags, rename the template tracks adding the prefix "deleted_" to the previous name.

deleteTempTableSize - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

DeleteTokensService - Class in org.intermine.webservice.server.user

Service which ensures that the authenticating user has no tokens.

DeleteTokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeleteTokensService

deleteUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices

Un-share the bag given in input with the user which userName is input

deleteWithConnection(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Performs a delete, with a connection.

deleteWithConnection(Connection, QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Performs a delete, with a connection.

DeletionEvent - Class in org.intermine.api.search

A representation of a notification that a websearchable has been deleted.

DeletionEvent(WebSearchable) - Constructor for class org.intermine.api.search.DeletionEvent

Constructor.

DeletionToken - Class in org.intermine.webservice.server.user

A class representing a deletion token.

DeletionToken(Profile, UUID, Date) - Constructor for class org.intermine.webservice.server.user.DeletionToken

DeletionTokenCancellationService - Class in org.intermine.webservice.server.user

A service that cancels the profile deletion process by deleting the token that could be used to complete it.

DeletionTokenCancellationService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenCancellationService

DeletionTokenInfoService - Class in org.intermine.webservice.server.user

A service that retrieves information about a deletion token.

DeletionTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenInfoService

DeletionTokens - Class in org.intermine.webservice.server.user

A class that manages deletion tokens for the lifespan of a webapp.

DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser

The string that delimits the sections of the NotXml.

DelimitedFileConfiguration - Class in org.intermine.task

This class specifies how the values in a tab or comma separated file should be used to fill in objects in an ObjectStore.

DelimitedFileConfiguration(Model, InputStream) - Constructor for class org.intermine.task.DelimitedFileConfiguration

Create a new DelimitedFileConfiguration from an InputStream.

deregisterRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

This method deregisters a Thread from a request ID.

deregisterStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

This method deregisters a Statement for the request ID of the current thread.

DeregistrationService - Class in org.intermine.webservice.server.user

DeregistrationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeregistrationService

DeregistrationTokenServlet - Class in org.intermine.webservice.server.user

A servlet for routing requests to do with deregistration.

DeregistrationTokenServlet() - Constructor for class org.intermine.webservice.server.user.DeregistrationTokenServlet

description - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

description - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

DESCRIPTION_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

The description

deSelectId(String, String) - Static method in class org.intermine.dwr.AjaxServices

remove an Id from the PagedTable

deSelectId(Integer) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Remove the object with the given object id from the list of selected objects.

destDir - Variable in class org.intermine.task.ModelOutputTask

destDir - Variable in class org.intermine.task.RetrieveMetadataTask

destFile - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask

destroy() - Method in class org.intermine.web.filters.ExpiresHeaderFilter

destroy() - Method in class org.intermine.web.filters.HeaderFilter

destroy() - Method in class org.intermine.web.filters.ReleaseEtagFilter

destroy() - Method in class org.intermine.web.filters.SetCharacterEncodingFilter

Take this filter out of service.

destroy() - Method in class org.intermine.web.struts.InitialiserPlugin

Destroy method called at Servlet destroy.

destroy() - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter

destroy() - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet

deVerify() - Method in class org.intermine.pathquery.PathQuery

DevNullMap<K,V> - Class in org.intermine.api.util

An implementation of Map that is totally forgetful.

DevNullMap() - Constructor for class org.intermine.api.util.DevNullMap

didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Internal method that records that a query was not explained.

didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose

Internal method that records that a query was not explained.

diff(ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Find the symmetric difference of one or more lists to produce a new list.

diff(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Find the symmetric difference of one or more lists to produce a new list.

diff(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Find the symmetric difference of one or more lists to produce a new list.

diff(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Find the symmetric difference of one or more lists to produce a new list.

DirectDataLoader - Class in org.intermine.dataloader

A DataLoader with helper methods for creating and storing objects using an IntegrationWriter.

DirectDataLoader(IntegrationWriter, String, String) - Constructor for class org.intermine.dataloader.DirectDataLoader

Create a new DirectDataLoader using the given IntegrationWriter and source name.

DirectDataLoaderTask - Class in org.intermine.task

This task uses a DirectDataLoader to create objects and store them directly into an ObjectStore using an IntegrationWriter.

DirectDataLoaderTask() - Constructor for class org.intermine.task.DirectDataLoaderTask

DirectoryConverter - Class in org.intermine.dataconversion

Parent class for DataConverters that read from directories

DirectoryConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DirectoryConverter

Constructor

DirectoryConverterTask - Class in org.intermine.task

Initiates retrieval and conversion of data from a source directory.

DirectoryConverterTask() - Constructor for class org.intermine.task.DirectoryConverterTask

disableResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

disableSaving() - Method in class org.intermine.api.profile.Profile

Disable saving until enableSaving() is called.

DisclosureBodyTag - Class in org.intermine.web.tags.disclosure

This class renders disclosureBody tag.

DisclosureBodyTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureBodyTag

DisclosureDetailsTag - Class in org.intermine.web.tags.disclosure

This class renders disclosureDetails tag.

DisclosureDetailsTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureDetailsTag

DisclosureHeadTag - Class in org.intermine.web.tags.disclosure

This class renders disclosureHead tag.

DisclosureHeadTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureHeadTag

DisclosureTag - Class in org.intermine.web.tags.disclosure

This class renders disclosure tag.

DisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTag

DisclosureTitleTag - Class in org.intermine.web.tags.disclosure

This class renders disclosureTitle tag.

DisclosureTitleTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTitleTag

display(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer

To be implemented in subclasses where any specific information to be displayed should be put on the request.

DisplayCollection - Class in org.intermine.web.logic.results

Class to represent a collection field of an object for the webapp

DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayCollection

Construct a new DisplayCollection object

DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayCollection

Construct a DisplayCollection object.

DisplayConstraint - Class in org.intermine.web.logic.query

Representation of a PathQuery constraint for use by JSP pages.

DisplayConstraint(Path, Profile, PathQuery, AutoCompleter, ObjectStoreSummary, BagQueryConfig, Map<String, List<FieldDescriptor>>, BagManager) - Constructor for class org.intermine.web.logic.query.DisplayConstraint

Construct for a new constraint that is being added to a query.

DisplayConstraint.DisplayConstraintOption - Class in org.intermine.web.logic.query

Representation of a constraint operation to populate a dropdown.

DisplayConstraint.DisplayConstraintOption(String, Integer) - Constructor for class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption

Construct with the constraint lable and index

DisplayConstraintFactory - Class in org.intermine.web.logic.query

A class that will help you manufacture instances of DisplayConstraint.

DisplayConstraintFactory(InterMineAPI, AutoCompleter) - Constructor for class org.intermine.web.logic.query.DisplayConstraintFactory

Get an object that creates display constraints.

DisplayConstraintHelpMessages - Class in org.intermine.web.logic.query

Class to generate help messages appropriate to a given constraint for display in the QueryBuilder and template form.

Displayer - Class in org.intermine.web.logic.config

Configuration object describing details of a displayer

Displayer() - Constructor for class org.intermine.web.logic.config.Displayer

DisplayerManager - Class in org.intermine.web.displayer

Read in and provide access to report page displayers.

DisplayField - Class in org.intermine.web.logic.results

Class to represent a field of an object for the webapp

DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayField

Create a new DisplayField object.

DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayField

Create a new DisplayField object.

DisplayLookupMessageHandler - Class in org.intermine.web.struts

DisplayLookupMessageHandler() - Constructor for class org.intermine.web.struts.DisplayLookupMessageHandler

DisplayPath - Class in org.intermine.web.logic.querybuilder

A small wrapper around Path with more jsp-accessible data.

DisplayPath(Path) - Constructor for class org.intermine.web.logic.querybuilder.DisplayPath

Constructs a new DisplayPath object from a Path.

DisplayReference - Class in org.intermine.web.logic.results

Class to represent a reference field of an object for display in the webapp

DisplayReference(ProxyReference, ReferenceDescriptor, WebConfig, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.web.logic.results.DisplayReference

Create a new DisplayReference object.

distinct - Variable in class org.intermine.sql.query.Query

DIVIDE - Static variable in class org.intermine.objectstore.query.QueryExpression

Division of two numeric fields

DIVIDE - Static variable in class org.intermine.sql.query.Function

DIVIDE function - takes two operands.

DO_NOTHING_ACTION - Static variable in class org.intermine.bio.dataconversion.SequenceProcessor

An action that does nothing - used to ignore a synonym/dbxref/whatever instead of doing the default.

doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.pathquery.PathQueryBinding

Adds any extra information for a constraint, like say Template extras.

doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.template.xml.TemplateQueryBinding

Adds any extra information for a constraint, like say Template extras.

doAnalyse(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs an ANALYSE of a table.

doDelete(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet

doDeletes(String, TableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs all the deletes for the given table name and table batch.

doesNotContain(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to not contain a value.

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ExpiresHeaderFilter

Add an expires header to matching files to help browsers avoid reloading static files.

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.HeaderFilter

Do the filtering.

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ReleaseEtagFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter

Select and set (if specified) the character encoding to be used to interpret request parameters for this request.

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter

doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Finalise this object.

doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Overrides Object.finalize - release the connection back to the objectstore.

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ClassKeyServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SchemaServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SummaryServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.TokenServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet

}

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet

}

doIndirectionDeletes(String, IndirectionTableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs all the delete operations for the given IndirectionTableBatch and name.

doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

Performs all the insert operations for the given IndirectionTableBatch and name.

doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl

Performs all the insert operations for the given IndirectionTableBatch and name.

doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs all the insert operations for the given IndirectionTableBatch and name.

doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

Performs all the inserts for the given table name and table batch.

doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl

Performs all the inserts for the given table name and table batch.

doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs all the inserts for the given table name and table batch.

doLogin(HttpServletRequest, String, String) - Method in class org.intermine.web.logic.profile.LoginHandler

Log-in a user.

doMarshal(PathQuery, String, String, XMLStreamWriter, int) - Method in class org.intermine.pathquery.PathQueryBinding

Marshal to an XMLStreamWriter.

doMarshal(TemplateQuery, XMLStreamWriter, int) - Method in class org.intermine.template.xml.TemplateQueryBinding

Convert a TemplateQuery to XML and write XML to given writer.

DoNothingAction - Class in org.intermine.bio.chado.config

An action that does nothing.

DoNothingAction() - Constructor for class org.intermine.bio.chado.config.DoNothingAction

DoNothingIdResolver - Class in org.intermine.bio.dataconversion

An IdResolver for use in tests that will always resolve an id to the input id given.

DoNothingIdResolver(String) - Constructor for class org.intermine.bio.dataconversion.DoNothingIdResolver

Construct and empty IdResolver

DoNothingIdResolverFactory - Class in org.intermine.bio.dataconversion

Construct a DoNothingIdResolver that will resolve every id to the id that was given as input.

DoNothingIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.DoNothingIdResolverFactory

Construct with class name for mock IdResolver

doPk(PrimaryKey, ClassDescriptor, Map<InterMineObject, Set<InterMineObject>>, List<InterMineObject>, Set<Integer>) - Method in class org.intermine.dataloader.BatchingFetcher

Fetches equivalent objects for a particular primary key.

doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.BatchingFetcher

Fetches data for the given primary keys.

doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.ParallelBatchingFetcher

Fetches data for the given primary keys.

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet

}

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet

}

doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet

}

doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet

doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet

doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet

doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet

doQueryGetPagedTable(HttpServletRequest, InterMineBag) - Static method in class org.intermine.web.logic.session.SessionMethods

Execute a query and return a PagedTable to display contents of an InterMineBag

doQueryGetPagedTable(HttpServletRequest, InterMineObject, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods

Execute a query and return a PagedTable to display contents of a Collection, field of a given InterMineObject.

doReplace() - Method in class org.intermine.webservice.server.lists.ListInput

doRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager

Returns when the given request is completed.

doRequest(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager

Returns the batch described by the request.

doShutdown() - Static method in class org.intermine.web.context.InterMineContext

Send the signal that shutdown is happening - try and release resources.

doSQL(ObjectStore) - Method in class org.intermine.task.ConverterTask

Runs various performance-enhancing SQL statements.

doStaticLogin(HttpServletRequest, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler

Main log-in logic.

doSummarise - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag

Renders tag.

doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag

Renders tag.

doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag

Renders tag.

doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Renders tag.

doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag

Renders tag.

doTag() - Method in class org.intermine.web.tags.table.NavigationBarTag

According pageSize and currentPage parameter navigation bar computes link to following and previous page.

doTag() - Method in class org.intermine.web.tags.table.TableTag

doTag() - Method in class org.intermine.web.tags.util.TreatStringTag

doTrackerFor(Class<?>) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Returns true if the given class is NOT a subclass of any of the classes in trackerMissingClasses.

doUpgrade() - Method in interface org.intermine.api.bag.IdUpgrader

Return true if upgrade should be performed

doUpgrade() - Method in class org.intermine.web.bag.PkQueryIdUpgrader

Return true if upgrade should be performed.

download(String) - Method in class org.intermine.web.util.HttpClient

doWrite() - Method in class org.intermine.dataloader.DataTracker

Performs maintenance of the cache, writing stuff to the backing database.

drainToPrintStream(PrintStream) - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Sends the entire contents of the Clob into the given PrintStream.

drainToPrintStream(PrintStream) - Method in class org.intermine.objectstore.query.ClobAccess

Sends the entire contents of the Clob into the given PrintStream.

driver - Variable in class org.intermine.sql.Database

dropAffected(Set<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Deletes all precomputed tables that would be affected by changes in any table in a given list of table names.

dropEverything() - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Deletes every single precomputed table.

dropIndex(WebSearchable) - Method in class org.intermine.api.search.SearchRepository

Drop the index that contains information about the websearchable object passed in.

dropIndex(String, int) - Method in class org.intermine.task.CreateIndexesTask

Drop an index by name, ignoring any resulting errors

DropPrecomputedTablesTask - Class in org.intermine.task

A Task that drops all precomputed tables in an ObjectStore.

DropPrecomputedTablesTask() - Constructor for class org.intermine.task.DropPrecomputedTablesTask

DummyExplainResult - Class in org.intermine.sql.query

Subclass of ExplainResult not associated with a database.

DummyExplainResult(Query) - Constructor for class org.intermine.sql.query.DummyExplainResult

Constructs an instance of PostgresExplainResult without any data.

DumpDefaultTemplatesTask - Class in org.intermine.web.task

Dump templates and configuration tags.

DumpDefaultTemplatesTask() - Constructor for class org.intermine.web.task.DumpDefaultTemplatesTask

DUPLICATE - Static variable in class org.intermine.api.bag.BagQueryResult

Key of the Map returned by getIssues() when the query for the input string found more than one object.

DuplicateMappingException - Exception in org.intermine.api.profile

DuplicateMappingException(String, String) - Constructor for exception org.intermine.api.profile.DuplicateMappingException

duplicateObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

This is a list of the objects in the destination database that we have written to as a non-skeleton more than once.

DynamicAttributeTask - Class in org.intermine.task

An ant task that provides a method for setting attributes dynamically within a class.

DynamicAttributeTask() - Constructor for class org.intermine.task.DynamicAttributeTask

DynamicBean - Class in org.intermine.util

Class which represents a generic bean

DynamicBean() - Constructor for class org.intermine.util.DynamicBean

Construct the interceptor

DynamicUtil - Class in org.intermine.util

Utilities to create DynamicBeans

E

earlyExtraProcessing(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Do any extra processing that is needed before the converter starts querying features

earlyExtraProcessing(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Do any extra processing that is needed before the converter starts querying features

earlyItems - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

editable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

editableConstraints - Variable in class org.intermine.template.TemplateQuery

List of those Constraints that are editable

editConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Edit a constraint on the query identified by the constraint code.

edited - Variable in class org.intermine.template.TemplateQuery

Whether this is an edited version of another template.

EDITING_TEMPLATE - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the status editing template

editJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Edit a the join style settings for a path.

EditPropertiesAction - Class in org.intermine.web.struts

A controller to edit the properties of a running application.

EditPropertiesAction() - Constructor for class org.intermine.web.struts.EditPropertiesAction

EditPropertiesForm - Class in org.intermine.web.struts

An overly verbose way of passing parameters back to the controller.

EditPropertiesForm() - Constructor for class org.intermine.web.struts.EditPropertiesForm

EditTemplateAction - Class in org.intermine.web.struts

Action to edit a user template query.

EditTemplateAction() - Constructor for class org.intermine.web.struts.EditTemplateAction

editTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Edit a constraint's template settings identified by code in query.

EFETCH_URL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Either<A,B> - Class in org.intermine.webservice.server.core

Disjoint type union Disjoint type union to handle certain features of the way we present results in outer-joined tables, but abstracted to be made more generally useful, and incorportating the visitor pattern for value access.

Either.Left<A,B> - Class in org.intermine.webservice.server.core

Either.Left(A) - Constructor for class org.intermine.webservice.server.core.Either.Left

Construct a left.

Either.Right<A,B> - Class in org.intermine.webservice.server.core

Either.Right(B) - Constructor for class org.intermine.webservice.server.core.Either.Right

Construct a right.

EitherVisitor<A,B,T> - Class in org.intermine.webservice.server.core

A mapping function capable of accessing a disjoint sum-type (an Either A B).

EitherVisitor() - Constructor for class org.intermine.webservice.server.core.EitherVisitor

EMAIL - Static variable in class org.intermine.api.profile.UserPreferences

This is known to the API as the Profile needs to read this to provide getEmailAddress().

email(String, String) - Method in class org.intermine.util.Emailer

Send a message to a user.

email(String, String, Object...) - Method in class org.intermine.util.Emailer

Send a message to a user with some data.

email(String, String, String, String, Properties) - Static method in class org.intermine.util.MailUtils

Send an email to an address, supplying the recipient, subject and body.

email(String, String, String, Properties) - Static method in class org.intermine.util.MailUtils

email(String, String) - Method in class org.intermine.web.context.NullMailer

email(String, String, Object...) - Method in class org.intermine.web.context.NullMailer

Emailer - Class in org.intermine.util

A class that will send emails to people.

Emailer(Properties) - Constructor for class org.intermine.util.Emailer

Instantiate an emailer.

EmailerFactory - Class in org.intermine.web.context

emailPasswordToken(String, String, Properties) - Static method in class org.intermine.util.MailUtils

Send a password change email to an email address

emptyAttributesMap - Variable in class org.intermine.objectstore.ObjectStoreSummary

emptyFieldsMap - Variable in class org.intermine.objectstore.ObjectStoreSummary

enableSaving() - Method in class org.intermine.api.profile.Profile

Re-enable saving when saveTemplate(), deleteQuery() etc. are called.

enableSaving() - Method in class org.intermine.api.util.AnonProfile

EncloseSubqueryBestQuery - Class in org.intermine.sql.precompute

This object is a BestQuery tracker that encloses all added queries into a surrounding query as a subquery, and passes them onto another BestQuery tracker.

EncloseSubqueryBestQuery(BestQuery, String, String) - Constructor for class org.intermine.sql.precompute.EncloseSubqueryBestQuery

Constructor.

encode(Object) - Static method in class org.intermine.webservice.server.LinkGeneratorBase

Encodes object string value to be able to be part of url.

encode(Object) - Static method in class org.intermine.webservice.server.query.result.QueryResultService

URL Encode an object.

ENCODED_DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser

The character that denotes an encoded delimiter in the string.

encodeString(String) - Static method in class org.intermine.web.util.URLUtil

Encodes string to be URL safe.

encodeURL(String) - Static method in class org.intermine.web.util.URLUtil

Encodes URL.

encoding - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter

The default character encoding to set for requests that pass through this filter.

end - Variable in class org.intermine.objectstore.query.OverlapRange

endDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler

endElement(String, String, String) - Method in class org.intermine.api.bag.BagQueryHandler

endElement(String, String, String) - Method in class org.intermine.api.bag.InvitationHandler

endElement(String, String, String) - Method in class org.intermine.api.profile.PreferencesHandler

endElement(String, String, String) - Method in class org.intermine.api.profile.TagHandler

endElement(String, String, String) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler

endElement(String, String, String) - Method in class org.intermine.api.xml.InterMineBagHandler

endElement(String, String, String) - Method in class org.intermine.api.xml.SavedQueryHandler

endElement(String, String, String) - Method in class org.intermine.api.xml.SharedBagHandler

endElement(String, String, String) - Method in class org.intermine.pathquery.PathQueryHandler

endElement(String, String, String) - Method in class org.intermine.template.xml.TemplateQueryHandler

endElement(String, String, String) - Method in class org.intermine.webservice.server.ServiceListingHandler

endElement(String, String, String) - Method in class org.intermine.xml.full.FullHandler

endIsAttribute() - Method in class org.intermine.pathquery.Path

Return true if and only if the end of the path is an attribute.

endIsCollection() - Method in class org.intermine.pathquery.Path

Return true if and only if the end of the path is a collection.

endIsReference() - Method in class org.intermine.pathquery.Path

Return true if and only if the end of the path is a reference .

endl - Variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

ENDL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

ENDL - Static variable in class org.intermine.bio.dataconversion.PdbConverter

ENDL - Static variable in class org.intermine.codegen.JavaModelOutput

ENDL - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput

ENDL - Static variable in class org.intermine.xml.full.FullRenderer

EnrichmentCalculation - Class in org.intermine.web.logic.widget

Calculate enrichment of an attribute applied to members of a sample that is a subset of a larger population.

EnrichmentInput - Interface in org.intermine.web.logic.widget

Define methods to access data an enrichment calculation needs to be provided with.

EnrichmentInputWidgetLdr - Class in org.intermine.web.logic.widget

Executes queries and summarises data for a specific EnrichmentWidgetLdr ready for calculation.

EnrichmentInputWidgetLdr(ObjectStore, EnrichmentWidgetImplLdr) - Constructor for class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

Construct with an EnrichmentWidgetLdr that contains queries needed for specific widget tests.

EnrichmentJSONProcessor - Class in org.intermine.webservice.server.widget

EnrichmentOptions - Interface in org.intermine.web.logic.widget

The type of options that enrichment widgets expect to receive.

EnrichmentResultProcessor - Interface in org.intermine.webservice.server.widget

The type of objects that can process enrichment results for serialisation to the outside world.

EnrichmentResults - Class in org.intermine.web.logic.widget

A container for results from an Enrichment analysis.

EnrichmentResults(Map<String, BigDecimal>, Map<String, Integer>, Map<String, String>, int) - Constructor for class org.intermine.web.logic.widget.EnrichmentResults

Construct with pre-populated maps from enriched attributes to p-values, counts and labels.

EnrichmentWidget - Class in org.intermine.web.logic.widget

EnrichmentWidget(EnrichmentWidgetConfig, InterMineBag, InterMineBag, ObjectStore, EnrichmentOptions) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidget

EnrichmentWidgetConfig - Class in org.intermine.web.logic.widget.config

A description of an enrichment calculation.

EnrichmentWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

EnrichmentWidgetForm - Class in org.intermine.web.struts

EnrichmentWidgetForm() - Constructor for class org.intermine.web.struts.EnrichmentWidgetForm

Constructor

EnrichmentWidgetImplLdr - Class in org.intermine.web.logic.widget

Implement methods to access data an enrichment calculation needs to be provided with.

EnrichmentWidgetImplLdr(InterMineBag, InterMineBag, ObjectStore, EnrichmentWidgetConfig, String, boolean, CorrectionCoefficient) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

Construct an Enrichment widget loader, which performs the queries needed for enrichment statistics.

EnrichmentWidgetResultService - Class in org.intermine.webservice.server.widget

Web service that returns the result of an enrichment calculation over a list of objects.

EnrichmentWidgetResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

EnrichmentXMLProcessor - Class in org.intermine.webservice.server.widget

A widget result processor for enrichment results that produces output as XML.

ensemblDb - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

EnsemblIdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolverFactory for human Ensembl gene ids, this doesn't include any synonyms or id tracking but simply filters for ids that are located on a the main chromosomes.

EnsemblIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.EnsemblIdResolverFactory

Construct without SO term of the feature type.

ensemblIds - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

ensureBagIsDeleted(Profile, String) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

After this method returns, the will be no bag with the given name in the given profile.

entrez - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

EntrezGeneIdResolverFactory - Class in org.intermine.bio.dataconversion

ID resolver for Entrez genes.

EntrezGeneIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Constructor read pid configuration

EntrezOrganismRetriever - Class in org.intermine.bio.dataconversion

Class to fill in organism information using Entrez.

EntrezOrganismRetriever() - Constructor for class org.intermine.bio.dataconversion.EntrezOrganismRetriever

EntrezPublicationsRetriever - Class in org.intermine.bio.dataconversion

Class to fill in all publication information from pubmed

EntrezPublicationsRetriever() - Constructor for class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

entrySet() - Method in class org.intermine.api.profile.UserPreferences

entrySet() - Method in class org.intermine.api.util.DevNullMap

entrySet() - Method in class org.intermine.util.AlwaysMap

entrySet() - Method in class org.intermine.util.IdentityMap

entrySet() - Method in class org.intermine.util.ReferenceMap

entrySet() - Method in class org.intermine.webservice.client.results.JsonRowMap

entrySet() - Method in class org.intermine.webservice.client.results.ResultRowMap

eof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

eq(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be equal to a value.

EQ - Static variable in class org.intermine.sql.query.Constraint

An operation for this constraint indicating that left is equal to right.

EQUAL - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes one constraint as being equal to another constraint.

EQUAL - Static variable in class org.intermine.sql.query.AbstractValue

Describes two AbstractValues as being equal.

equals(Object) - Method in class org.intermine.api.bag.BagQueryResult.IssueResult

equals(Object) - Method in class org.intermine.api.bag.SharingInvite

equals(Object) - Method in class org.intermine.api.beans.ObjectDetails

equals(Object) - Method in class org.intermine.api.beans.PartnerLink

equals(Object) - Method in class org.intermine.api.idresolution.ResolutionJob

equals(Object) - Method in class org.intermine.api.mines.ObjectRequest

equals(Object) - Method in class org.intermine.api.profile.BagValue

Two bag values are identical if they have the same value and extra value.

equals(Object) - Method in class org.intermine.api.profile.SavedQuery

Test receiver for equality with passed object.

equals(Object) - Method in class org.intermine.api.results.Column

equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue

equals(Object) - Method in class org.intermine.api.results.ResultElement

equals(Object) - Method in class org.intermine.api.template.ApiTemplate

equals(Object) - Method in class org.intermine.bio.chado.ChadoCVTerm

equals(Object) - Method in class org.intermine.bio.ontology.OboTermSynonym

equals(Object) - Method in class org.intermine.bio.util.OrganismData

equals(Object) - Method in class org.intermine.objectstore.query.BagConstraint

equals(Object) - Method in class org.intermine.objectstore.query.ClassConstraint

Tests whether two ClassConstraints are equal.

equals(Object) - Method in class org.intermine.objectstore.query.Clob

Override Object#equals.

equals(Object) - Method in class org.intermine.objectstore.query.ConstraintSet

Test whether two ConstraintSets are equal, overrides Object.equals().

equals(Object) - Method in class org.intermine.objectstore.query.ContainsConstraint

Test whether two ContainsConstraints are equal, overrides Object.equals()

equals(Object) - Method in class org.intermine.objectstore.query.iql.IqlQuery

equals(Object) - Method in class org.intermine.objectstore.query.MultipleInBagConstraint

equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBag

Override Object#equals.

equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject

equals(Object) - Method in class org.intermine.objectstore.query.OverlapConstraint

equals(Object) - Method in class org.intermine.objectstore.query.PathExpressionField

equals(Object) - Method in class org.intermine.objectstore.query.QueryCast

equals(Object) - Method in class org.intermine.objectstore.query.QueryField

Returns true if this is equal to the given object.

equals(Object) - Method in class org.intermine.objectstore.query.QueryValue

Overrides Object.

equals(Object) - Method in class org.intermine.objectstore.query.Results

equals(Object) - Method in class org.intermine.objectstore.query.ResultsInfo

equals(Object) - Method in class org.intermine.objectstore.query.SimpleConstraint

Test whether two SimpleConstraints are equal, overrides Object.equals()

equals(Object) - Method in class org.intermine.objectstore.query.SubqueryConstraint

Test whether two SubqueryConstraints are equal, overrides Object.equals()

equals(Object) - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint

Test whether two SubqueryConstraints are equal, overrides Object.equals()

equals(Object) - Method in class org.intermine.pathquery.LogicExpression

equals(Object) - Method in class org.intermine.pathquery.Node

equals(Object) - Method in class org.intermine.pathquery.OrderElement

equals(Object) - Method in class org.intermine.pathquery.Path

equals(Object) - Method in class org.intermine.pathquery.PathQuery

equals(Object) - Method in class org.intermine.sql.precompute.PrecomputedTable

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.AbstractConstraint

Overrides Object.equals();

equals(Object) - Method in class org.intermine.sql.query.AbstractTable

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.AbstractValue

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.Constant

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.ExplainResult

equals(Object) - Method in class org.intermine.sql.query.Field

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.Function

Overrides Object.equals.

equals(Object) - Method in class org.intermine.sql.query.OrderDescending

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.Query

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.SelectValue

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.SubQuery

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.query.Table

Overrides Object.equals().

equals(Object) - Method in class org.intermine.sql.writebatch.Row

equals(Object) - Method in class org.intermine.template.TemplateQuery

equals(Object) - Method in class org.intermine.util.AlwaysMap

equals(Object) - Method in class org.intermine.util.IdentityMap

equals(Object) - Method in class org.intermine.util.ReferenceMap

equals(Object) - Method in class org.intermine.web.logic.config.Displayer

equals(Object) - Method in class org.intermine.web.logic.config.FieldConfig

equals(Object) - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart

equals(Object) - Method in class org.intermine.web.logic.config.TableExportConfig

equals(Object) - Method in class org.intermine.web.logic.config.Type

equals(Object) - Method in class org.intermine.web.logic.config.WebConfig

equals(Object) - Method in class org.intermine.web.logic.template.ConstraintInput

equals(Object) - Method in class org.intermine.web.logic.TreeNode

equals(Object) - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

equals(Object) - Method in class org.intermine.webservice.client.results.Item

Determine whether this object is equal to the other.

equals(Object) - Method in class org.intermine.webservice.client.results.Page

equals(Object) - Method in class org.intermine.webservice.server.core.Either

equals(Object) - Method in class org.intermine.webservice.server.JWTBuilder

equals(Object) - Method in class org.intermine.xml.full.Attribute

equals(Object) - Method in class org.intermine.xml.full.Item

equals(Object) - Method in class org.intermine.xml.full.Reference

equals(Object) - Method in class org.intermine.xml.full.ReferenceList

equalsExactly(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be exactly equal to a value.

equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable

Compare this AbstractTable to another, ignoring little details like aliases.

equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.SubQuery

Compare this SubQuery to another AbstractTable, ignoring alias.

equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.Table

Compare this Table to another AbstractTable, ignoring alias.

equalsNoUnion(Object) - Method in class org.intermine.sql.query.Query

Returns true if this Query is equivalent to obj, disregarding other queries in the UNION.

equalsOnlyAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable

Compare this AbstractTable to another, only comparing the alias.

equalsTableOnlyAlias(AbstractValue) - Method in class org.intermine.sql.query.Field

Compare this Field to another AbstractValue, including only the table alias.

equalToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be equal to a loopPath.

EquivalentObjectFetcher - Interface in org.intermine.dataloader

Interface providing methods to look up equivalent objects by primary key in a production objectstore.

EquivalentObjectHints - Class in org.intermine.dataloader

Object for holding hint data for the getEquivalentObjects method in IntegrationWriters.

EquivalentObjectHints(ObjectStore) - Constructor for class org.intermine.dataloader.EquivalentObjectHints

Constructor.

equivalents - Variable in class org.intermine.dataloader.BatchingFetcher

error(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

}

ERROR_CODE - Static variable in exception org.intermine.webservice.client.exceptions.ServiceException

ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter

The string that begins an error line.

ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.PlainFormatter

The string that begins an error line.

ERROR_UPGRADER - Static variable in interface org.intermine.api.bag.IdUpgrader

An upgrader that always fails.

ErrorCorrection - Class in org.intermine.web.logic.widget

See online help docs for detailed description of what error correction is and why we need it.

ErrorCorrection.Strategy - Enum in org.intermine.web.logic.widget

ErrorMessageParser - Class in org.intermine.webservice.client.util

Parses service error message.

ErrorMessagesController - Class in org.intermine.web.struts

Take the messages stored in the session which are not using ActionMessages or ActionErrors and put them in the request

ErrorMessagesController() - Constructor for class org.intermine.web.struts.ErrorMessagesController

ERRORS - Static variable in class org.intermine.web.logic.Constants

Session attribute that temporarily holds a Vector of errors that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows errors after redirect).

escapeAttribute(Object) - Method in class org.intermine.webservice.server.output.XMLFormatter

escapeElementContent(String) - Method in class org.intermine.webservice.server.output.XMLFormatter

Escape the content of an element.

escapeReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts words into escaped form.

estimate(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Explain a Query (give estimate for execution time and number of rows).

estimate(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Explain a Query (give estimate for execution time and number of rows).

estimate(Query) - Method in interface org.intermine.objectstore.ObjectStore

Explain a Query (give estimate for execution time and number of rows).

estimate(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Explain a Query (give estimate for execution time and number of rows).

ESTIMATE - Static variable in class org.intermine.objectstore.query.ResultsInfo

Denotes that the result of getRows() is a pure estimate that is not contradicted by the min or max

estimate(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Explain a Query (give estimate for execution time and number of rows).

estimate(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Explain a Query (give estimate for execution time and number of rows).

estimatedRows - Variable in class org.intermine.sql.query.ExplainResult

estimateWithConnection(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Runs an EXPLAIN for the given query.

ESUMMARY_URL - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

ESUMMARY_URL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns whether optimisation should be permitted.

everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Returns whether optimisation should be permitted.

evictFromCache(Profile) - Method in class org.intermine.api.profile.ProfileManager

Remove a profile from the cache

EvictOrphansTask - Class in org.intermine.web.task

A task for removing tags that don't point to anything.

EvictOrphansTask() - Constructor for class org.intermine.web.task.EvictOrphansTask

evidence - Variable in class org.intermine.bio.dataconversion.UniprotEntry.Comment

EXCEPT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination

Constant representing an EXCEPT operation

EXCLUDES - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as being mutually exclusive.

execute(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor

Executes object store query and returns results as iterator over rows.

execute(PathQuery, int, int) - Method in class org.intermine.api.query.PathQueryExecutor

Executes object store query and returns results as iterator over rows.

execute(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.

execute(PathQuery, Map<String, BagQueryResult>) - Method in class org.intermine.api.query.WebResultsExecutor

Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.

execute() - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

For each Organism in the objectstore, retreive it's details from entrez using the taxon and fill in the details in the organism object.

execute() - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Synchronize publications with pubmed using pmid

execute() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

execute() - Method in class org.intermine.bio.dataconversion.UniprotFilterTask

execute() - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

Use the linkFile attribute (which is a file containing FlyBase Translation <-> UniProt accession numbers) to link Translation objects to Protein objects in the ObjectStoreWriter.

execute() - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask

execute() - Method in class org.intermine.bio.task.GFF3ConverterTask

execute() - Method in class org.intermine.bio.task.OboConverterTask

Run the task

execute() - Method in class org.intermine.bio.task.SOClassNameMapMakerTask

execute() - Method in class org.intermine.bio.task.SOToModelTask

execute(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute() - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

execute() - Method in class org.intermine.dataloader.XmlDataLoaderTask

execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute() - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask

execute(Query) - Method in interface org.intermine.objectstore.ObjectStore

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Execute a Query on this ObjectStore

execute(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Execute a Query on this ObjectStore

execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Execute a Query on this ObjectStore

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.

execute() - Method in class org.intermine.task.AcceptanceTestTask

execute() - Method in class org.intermine.task.AnalyseDbTask

execute() - Method in class org.intermine.task.BuildDbTask

execute() - Method in class org.intermine.task.CreateIndexesTask

execute(Connection, String) - Method in class org.intermine.task.CreateIndexesTask

Execute an sql statement.

execute() - Method in class org.intermine.task.DBConverterTask

Run the task

execute() - Method in class org.intermine.task.DirectDataLoaderTask

execute() - Method in class org.intermine.task.DirectoryConverterTask

Run the task.

execute() - Method in class org.intermine.task.DropPrecomputedTablesTask

execute() - Method in class org.intermine.task.FileConverterTask

Run the task

execute() - Method in class org.intermine.task.FullXmlConverterTask

execute() - Method in class org.intermine.task.GrantTask

execute() - Method in class org.intermine.task.ModelMergerTask

execute() - Method in class org.intermine.task.ModelOutputTask

execute() - Method in class org.intermine.task.PostProcessorTask

Run the task

execute() - Method in class org.intermine.task.PrecomputeTask

execute() - Method in class org.intermine.task.RetrieveMetadataTask

execute() - Method in class org.intermine.task.RunIqlQueryTask

execute() - Method in class org.intermine.task.StaticMethodTask

execute() - Method in class org.intermine.task.StoreMetadataTask

execute() - Method in class org.intermine.task.SummariseObjectStoreTask

execute(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer

Execute is called for each report page with the object to be displayed.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddColumnAction

Executes action.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddToBagAction

Save a single object to an existing bag.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiJavaController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiPerlController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AspectController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AvailableColumnsController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagBuildController

Set up environment for the buildBag page.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsAction

Set up session attributes for the bag details page.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUpgradeAction

Action for creating BagQueryResult for a specific bag not yet current

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmAction

Action to save a bag from the bagUploadConfirm page into the user profile.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmController

Set up the bagUploadConfirm page.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmIssueController

Initialise attributes for the bagUploadConfirmIssue.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BeginAction

Either display the query builder or redirect to project.sitePrefix.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BuildBagAction

Action for creating a bag of InterMineObjects or Strings from identifiers in text field.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangePasswordAction

Method called when user has finished filling out the 'change password' form

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableSizeAction

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ClassChooserController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionDetailsAction

Create PagedTable for this collection, register it with an identifier and redirect to results.do?

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionTableAction

Create PagedTable for this collection, register it with an identifier

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ContactAction

Method called when user has submitted valid feedback form

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ConvertBagController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CountTableController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateAccountAction

Method called when user has finished updating a constraint.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateTemplateAction

Take the current query and TemplateBuildState from the session and create a TemplateQuery.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CurrentQueryAction

Either display the query builder or redirect to project.sitePrefix.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditPropertiesAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditTemplateAction

Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ErrorMessagesController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportOptionsController

Set up the exportOptions tile.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportQueryAction

Method called to export a saved Query.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportTagsAction

Export user's tags.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FavouritesController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FileDownloadAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FindInListAction

Method called when user has submitted the search form.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GetAttributeAsFileAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GotoWebSearchableAction

Method called when user has submitted search form.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HeartbeatAction

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HintsController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HtmlHeadController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportQueriesAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportTagsAction

Import user's tags.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InlineTagEditorController

execute(Exception, ExceptionConfig, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineExceptionHandler

Handle the exception.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InvitationAction

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.KeywordSearchResultsController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LabelsSummaryAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginAction

Method called for login in

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginController

Set up the form for login.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LogoutAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagAction

Forward to the correct method based on the button pressed

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagDetailsAction

Forward to the correct method based on the button pressed

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction

Forward to the correct method based on the button pressed.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifySuperUserAction

Forward to the correct method based on the button pressed

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction

Forward to the correct method based on the button pressed.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.MyMineController

Set up attributes for the myMine page.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Authenticator

Method called for login in

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Callback

Method called for login in

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectTrailController

Looks at the "trail" request parameter and extracts the object ids from it, then looks up the actual objects and creates a list of TrailItems.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectViewController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetAction

Method called when the form is submitted.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetController

Set up the form.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PollQueryAction

Handle request from client.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PortalQueryAction

Link-ins from other sites end up here (after some redirection).

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintAction

Method called when user has finished updating a constraint.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderSummaryController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewAction

Run the query and forward to the results page.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryClassSelectAction

Add a QueryClass of a specified type to the current query.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportAspectController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportDisplayerController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportInListController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportTemplateController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RequestPasswordAction

Method called when user has finished updating a constraint

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ResultsAction

Called before results table is rendered.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RunQueryAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveFromIdsToBagAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveQueryAction

Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SharingBagUsersController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SubMenuController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SummariseTemplatesAction

Summarises every public template, and then forwards to the mymine template page.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableController

Set up table tile.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableExportAction

Method called to export a PagedTable object.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateAction

Build a query based on the template and the input from the user.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateController

Finds the correct template to display in the following ways: First, looks for a "name" request parameter and uses that for a the lookup.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateListController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateProblemsController

Called before template problem page is rendered.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesController

Set up attributes for the templates page.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesExportAction

Build a query based on the template and the input from the user.

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesImportAction

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeController

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TriageBagAction

Forward to the correct method based on the button pressed

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UsersController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebSearchableListController

Set up the attributes for webSearchableList.tile

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebserviceCodeGenAction

execute() - Method in class org.intermine.web.task.CreateSearchIndexTask

execute() - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Write templates and tags to a file.

execute() - Method in class org.intermine.web.task.EvictOrphansTask

execute() - Method in class org.intermine.web.task.IssueTokenTask

execute() - Method in class org.intermine.web.task.LoadBagValuesTask

Execute the task - load bagvalues table.

execute() - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Load templates from an xml file into a userprofile account.

execute() - Method in class org.intermine.web.task.ModelUpdateTask

Update savedquery, savedtemplatequery and savedbag in the userprofile through ModelUpdate object

execute() - Method in class org.intermine.web.task.PrecomputeTemplatesTask

execute() - Method in class org.intermine.web.task.ProfileReadTask

Execute the task - read the profiles.

execute() - Method in class org.intermine.web.task.ProfileWriteTask

Execute the task - write the profiles as XML.

execute() - Method in class org.intermine.web.task.TemplateTrackReadTask

Execute the task - read the profiles.

execute() - Method in class org.intermine.web.task.TemplateTrackWriteTask

Execute the task - write the template tracks as XML.

execute() - Method in class org.intermine.web.task.UpdateListTablesTask

Execute the task.

execute() - Method in class org.intermine.web.task.UpdateTrackTableTask

Execute the task - read the profiles.

execute() - Method in class org.intermine.web.task.VerifyTokenTask

execute() - Method in class org.intermine.webservice.server.branding.BrandingService

execute() - Method in class org.intermine.webservice.server.ClassKeysService

execute() - Method in class org.intermine.webservice.server.clob.SequenceService

execute() - Method in class org.intermine.webservice.server.data.DataService

execute() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService

execute() - Method in class org.intermine.webservice.server.idresolution.JobRemovalService

execute() - Method in class org.intermine.webservice.server.idresolution.JobResultsService

execute() - Method in class org.intermine.webservice.server.idresolution.JobStatusService

execute() - Method in class org.intermine.webservice.server.lists.AvailableListsService

execute() - Method in class org.intermine.webservice.server.lists.ListDeletionService

execute() - Method in class org.intermine.webservice.server.lists.ListMakerService

execute() - Method in class org.intermine.webservice.server.lists.ListRenameService

execute() - Method in class org.intermine.webservice.server.lists.ListShareCreationService

Runs service.

execute() - Method in class org.intermine.webservice.server.lists.ListShareDeletionService

execute() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService

execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService

execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService

execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService

execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService

execute() - Method in class org.intermine.webservice.server.lists.ListTagAddingService

execute() - Method in class org.intermine.webservice.server.lists.ListTagService

execute() - Method in class org.intermine.webservice.server.model.ModelService

Runs service.

execute() - Method in class org.intermine.webservice.server.path.PossibleValuesService

execute() - Method in class org.intermine.webservice.server.query.CodeService

execute() - Method in class org.intermine.webservice.server.query.QueryRemovalService

execute() - Method in class org.intermine.webservice.server.query.QueryRetrieverService

execute() - Method in class org.intermine.webservice.server.query.QueryStoreService

execute() - Method in class org.intermine.webservice.server.query.QueryToListService

execute() - Method in class org.intermine.webservice.server.query.QueryUploadService

execute() - Method in class org.intermine.webservice.server.query.result.QueryResultService

Executes service specific logic.

execute() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService

execute() - Method in class org.intermine.webservice.server.SchemaListService

execute() - Method in class org.intermine.webservice.server.search.QuickSearch

execute() - Method in class org.intermine.webservice.server.SessionService

execute() - Method in class org.intermine.webservice.server.SummaryService

execute() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService

execute() - Method in class org.intermine.webservice.server.template.result.TemplateResultService

Executes service specific logic.

execute() - Method in class org.intermine.webservice.server.template.SingleTemplateService

execute() - Method in class org.intermine.webservice.server.template.TemplateRemovalService

execute() - Method in class org.intermine.webservice.server.template.TemplateUploadService

execute() - Method in class org.intermine.webservice.server.user.DeletePreferencesService

execute() - Method in class org.intermine.webservice.server.user.DeleteTokensService

execute() - Method in class org.intermine.webservice.server.user.DeletionTokenCancellationService

execute() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService

execute() - Method in class org.intermine.webservice.server.user.DeregistrationService

execute() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService

execute() - Method in class org.intermine.webservice.server.user.NewUserService

execute() - Method in class org.intermine.webservice.server.user.PermaTokenDeletionService

execute() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService

execute() - Method in class org.intermine.webservice.server.user.ReadPreferencesService

execute() - Method in class org.intermine.webservice.server.user.SetPreferencesService

execute() - Method in class org.intermine.webservice.server.user.TokenService

execute() - Method in class org.intermine.webservice.server.user.TokensService

execute() - Method in class org.intermine.webservice.server.user.WhoAmIService

execute() - Method in class org.intermine.webservice.server.VersionService

execute() - Method in class org.intermine.webservice.server.WebService

Runs service.

execute() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService

execute() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

Executes service specific logic.

execute() - Method in class org.intermine.webservice.server.widget.GraphService

execute() - Method in class org.intermine.webservice.server.widget.TableWidgetService

executeRequest(Request) - Method in class org.intermine.webservice.client.core.Service

Open connection and returns connection.

executeSingleton(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in interface org.intermine.objectstore.ObjectStore

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Execute a Query on this ObjectStore, returning a SingletonResults

executeSqlInParallel(String) - Method in class org.intermine.sql.Database

Executes an SQL statement on the database in a separate thread.

executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Performs the actual execute, given a Connection.

executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>, Set<PrecomputedTable>, OptimiserCache) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Performs the actual execute, given a Connection.

existingBagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm

existingBagName - Variable in class org.intermine.web.struts.SaveBagForm

exists() - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint

Check whether a NOT NULL constraint was found.

expand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction

Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).

expandPath(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Given a path return a set of paths replacing a path with a '+' preceding a class name with an additional path for every subclass of that class.

experimentRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

EXPIRE_INTERVAL - Static variable in class org.intermine.sql.precompute.OptimiserCache

Number of events to happen before an expiration run.

ExpiresHeaderFilter - Class in org.intermine.web.filters

A Filter that modifies response headers of outgoing pages.

ExpiresHeaderFilter() - Constructor for class org.intermine.web.filters.ExpiresHeaderFilter

explain(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Explain a query and return estimates of execution time and row count.

explain - Variable in class org.intermine.objectstore.query.Results

explain - Variable in class org.intermine.sql.query.Query

explainResult - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

ExplainResult - Class in org.intermine.sql.query

Represents a result from an EXPLAIN request to a database.

ExplainResult() - Constructor for class org.intermine.sql.query.ExplainResult

export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.Exporter

Do export.

export(Iterator<? extends List<ResultElement>>) - Method in interface org.intermine.web.logic.export.Exporter

Perform the export with the exporter's defaults in the absence of path collection changes.

export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ExporterImpl

Do export.

export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.web.logic.export.ExporterImpl

export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter

Perform export.

export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter

Method called to export a PagedTable object

export(List<List<String>>) - Method in class org.intermine.web.logic.export.string.StringTableExporter

Perform export.

export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction

Load a template from template name passed as parameter.

export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction

Export the selected queries

export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction

Export the selected templates.

ExportController - Class in org.intermine.web.struts

Controller to initialise for the export.tile

ExportController() - Constructor for class org.intermine.web.struts.ExportController

Exporter - Interface in org.intermine.web.logic.export

Simple exporter interface.

ExporterImpl - Class in org.intermine.web.logic.export

Simple exporter exporting data as tab separated, comma separated and so.

ExporterImpl(OutputStream, RowFormatter) - Constructor for class org.intermine.web.logic.export.ExporterImpl

Constructor.

ExporterImpl(OutputStream, RowFormatter, String, List<String>) - Constructor for class org.intermine.web.logic.export.ExporterImpl

Constructor.

ExportException - Exception in org.intermine.web.logic.export

Exception thrown if the there is a problem while exporting (eg. from FieldExporter)

ExportException(String) - Constructor for exception org.intermine.web.logic.export.ExportException

Create a new ExportException.

ExportException(String, Exception) - Constructor for exception org.intermine.web.logic.export.ExportException

Create a new ExportException.

exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in interface org.intermine.web.logic.export.FieldExporter

Example FieldExporter that splits the a String field at the first comma and outputs each bit on a new line.

ExportHelper - Class in org.intermine.web.logic.export

Helper methods for exporters.

ExportOptionsController - Class in org.intermine.web.struts

Controller for exportOptions.tile

ExportOptionsController() - Constructor for class org.intermine.web.struts.ExportOptionsController

ExportQueryAction - Class in org.intermine.web.struts

Export the current query in XML format.

ExportQueryAction() - Constructor for class org.intermine.web.struts.ExportQueryAction

ExportResultsIterator - Class in org.intermine.api.results

An Iterator that produces data in a format suitable for exporting.

ExportResultsIterator(PathQuery, Query, Results, Map<String, QuerySelectable>) - Constructor for class org.intermine.api.results.ExportResultsIterator

Constructor for ExportResultsIterator.

ExportTagsAction - Class in org.intermine.web.struts

Export tags.

ExportTagsAction() - Constructor for class org.intermine.web.struts.ExportTagsAction

EXTRA_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

extra value parameter

EXTRA_VALUE_CONSTRAINT - Static variable in class org.intermine.api.config.Constants

Constrain by an extra value

extraAttribute - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

extraFieldValue - Variable in class org.intermine.web.struts.ModifyBagDetailsForm

extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Do any extra processing needed for this record (extra attributes, objects, references etc.)

extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask

Do any extra processing needed for this record (extra attributes, objects, references etc.)

extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

For objects that have primaryIdentifier == null, set the primaryIdentifier to be the uniquename column from chado.

extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask

Do any extra processing needed for this record (extra attributes, objects, references etc.)

extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Do any extra processing for this database, after all other processing is done

extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Do any extra processing for this database, after all other processing is done

ExtraQueryTime - Class in org.intermine.objectstore.intermine

An object that holds information about extra queries run during the ResultsConverter operation.

ExtraQueryTime() - Constructor for class org.intermine.objectstore.intermine.ExtraQueryTime

Constructor.

extraValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

F

F<A,B> - Class in org.intermine.webservice.server.core

A type for a function from A -> B.

F() - Constructor for class org.intermine.webservice.server.core.F

F.Constant<X,R> - Class in org.intermine.webservice.server.core

An implementation of a constant function.

F.Constant(R) - Constructor for class org.intermine.webservice.server.core.F.Constant

Construct a constant function.

FALSE - Static variable in class org.intermine.objectstore.query.QueryValue

The false value

fanOutCombinations(List<Collection<E>>) - Static method in class org.intermine.util.CollectionUtil

Returns a collection containing all possible combinations of the input values.

FastaLoaderTask - Class in org.intermine.bio.dataconversion

A task that can read a set of FASTA files and create the corresponding Sequence objects in an ObjectStore.

FastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FastaLoaderTask

fastSearch(String, String, int) - Method in class org.intermine.web.autocompletion.LuceneSearchEngine

Perform the search but only return n results.

fatalError(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

}

FavouritesController - Class in org.intermine.web.struts

Controller for the starTemplate tile.

FavouritesController() - Constructor for class org.intermine.web.struts.FavouritesController

featureMap - Variable in class org.intermine.bio.dataconversion.SequenceProcessor

fetchBatchFromObjectStore(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Gets a batch from the ObjectStore.

fetchByIds(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Class<?>, Collection<Integer>, ExtraQueryTime) - Static method in class org.intermine.objectstore.intermine.ResultsConverter

Fetches a group of objects from the database by ID.

fetchCollectionPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryCollectionPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter

Fetches the QueryCollectionPathExpression data for a query.

fetchObjectPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryObjectPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter

Fetches the contents of a QueryObjectPathExpression for a query.

field - Variable in class org.intermine.api.results.ResultElement

Field - Class in org.intermine.sql.query

A representation of a field in a table.

Field(String, AbstractTable) - Constructor for class org.intermine.sql.query.Field

Constructor for this Field object.

FieldConfig - Class in org.intermine.web.logic.config

The webapp configuration for one field of a class.

FieldConfig() - Constructor for class org.intermine.web.logic.config.FieldConfig

FieldConfigHelper - Class in org.intermine.web.logic.config

Helper methods for the FieldConfig class.

FieldExporter - Interface in org.intermine.web.logic.export

An interface implemented by objects that can export the value of a particular.

fieldIsPrimaryKey(Model, Class<?>, String, Source) - Static method in class org.intermine.dataloader.DataLoaderHelper

Returns true if the given field is a member of any primary key on the given class, for the given source.

fieldName - Variable in class org.intermine.objectstore.query.QueryForeignKey

fieldName - Variable in class org.intermine.objectstore.query.QueryReference

fields - Variable in class org.intermine.sql.logging.DatabaseWriter

file - Variable in class org.intermine.codegen.JavaModelOutput

file - Variable in class org.intermine.dataloader.XmlDataLoaderTask

file - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput

file - Variable in class org.intermine.task.FullXmlConverterTask

FileConverter - Class in org.intermine.dataconversion

Parent class for DataConverters that read from files

FileConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FileConverter

Constructor

FileConverterTask - Class in org.intermine.task

Initiates retrieval and conversion of data from a source file.

FileConverterTask() - Constructor for class org.intermine.task.FileConverterTask

FileDirectDataLoaderTask - Class in org.intermine.task

A DirectDataLoaderTask for files.

FileDirectDataLoaderTask() - Constructor for class org.intermine.task.FileDirectDataLoaderTask

FileDownloadAction - Class in org.intermine.web.struts

This is a generic action to download file from any given directory.

FileDownloadAction() - Constructor for class org.intermine.web.struts.FileDownloadAction

fileName - Variable in class org.intermine.web.task.DumpDefaultTemplatesTask

fileName - Variable in class org.intermine.web.task.ProfileWriteTask

fileName - Variable in class org.intermine.web.task.TemplateTrackWriteTask

FILENAME_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

The parameter for setting the filename

fileSet - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask

fileSet - Variable in class org.intermine.bio.task.GFF3ConverterTask

fileSet - Variable in class org.intermine.dataloader.XmlDataLoaderTask

fileSet - Variable in class org.intermine.task.FileConverterTask

fileSet - Variable in class org.intermine.task.FullXmlConverterTask

fileSets - Variable in class org.intermine.task.FileDirectDataLoaderTask

filter(BufferedReader, BufferedWriter) - Method in class org.intermine.bio.dataconversion.UniprotXmlFilter

Filter a UniProt XML dump file, write entries for organisms of interest to a new BufferedWriter.

filter(List<Constraint>, FromElement, boolean) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Return a subset of the given List that contains only Constraints that relate to the given FromElement or constraints associated with nothing if fromElement is null.

filter - Variable in class org.intermine.web.logic.widget.WidgetLdr

filter - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

filterByList(Map<String, WebSearchable>, String) - Static method in class org.intermine.web.struts.WebSearchableListController

Filters websearchables.

filterByTags(Map<String, W>, List<String>, String, String, TagManager) - Method in class org.intermine.api.search.SearchFilterEngine

Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.

filterByTags(Map<String, W>, List<String>, String, String, TagManager, boolean) - Method in class org.intermine.api.search.SearchFilterEngine

Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.

filterConfig - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter

The filter configuration object we are associated with.

FilteringResultIterator - Class in org.intermine.webservice.server.output

A result iterator that skips things we aren't interested in.

FilteringResultIterator(Results) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator

Construct a new iterator which does no filtering.

FilteringResultIterator(Results, int, int, String) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator

Construct a new iterator which filters to things that match a filter term and only returns results in a given window.

filterOutInvalidTemplates(Map<String, ? extends WebSearchable>) - Static method in class org.intermine.api.search.SearchResults

Filter out invalid templates from a map.

filterWebSearchables(String, String, List<String>, String, String, String) - Static method in class org.intermine.dwr.AjaxServices

Given a scope, type, tags and some filter text, produce a list of matching WebSearchable, in a format useful in JavaScript.

finalize() - Method in class org.intermine.api.tracker.TrackerDelegate

clean up threads

finalize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Overrides Object.finalize - release the DB log connection.

finalize() - Method in class org.intermine.sql.Database

find(Map<String, Object>) - Method in class org.intermine.webservice.client.lists.ItemList

Convenience method for finding members of a collection matching certain properties.

findAndCodes(Set<String>, LogicExpression.Node) - Static method in class org.intermine.api.query.MainHelper

Finds all the codes in a constraint logic that are ANDed in the given constraint logic.

findClassKeyValue(Map<String, List<FieldDescriptor>>, InterMineObject) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the first non-null class key field for the object with the given id.

findCombinations(Set<T>, Set<T>, Comparator<? super T>) - Static method in class org.intermine.util.MappingUtil

Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.

findCombinations(Set<T>, Set<T>, Comparator<? super T>, MappingUtilChecker<T>) - Static method in class org.intermine.util.MappingUtil

Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.

findCommonClasses(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

findCommonSuperclass(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil

Finds a common superclass or superinterface for all the classes specified in the arguments.

findCommonSuperclasses(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil

Finds common superclasses and superinterfaces for all the classes specified in the arguments.

findCommonSuperTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

Finds the common class for a set of classes.

findConnectingClasses(ObjectStore, Class<? extends FastPathObject>, String, Class<? extends FastPathObject>, String, Class<? extends FastPathObject>, boolean) - Static method in class org.intermine.bio.postprocess.PostProcessUtil

Return an iterator over the results of a query that connects two classes by a third using arbitrary fields.

findDuplicateSymbols(String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser

findForcedInnerJoins(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper

Get a list of paths that should be forced to inner join.

FindInListAction - Class in org.intermine.web.struts

Action to search a list for an identifier and then highlight it on the list details page.

FindInListAction() - Constructor for class org.intermine.web.struts.FindInListAction

FindInListForm - Class in org.intermine.web.struts

Form for FindInListAction.

FindInListForm() - Constructor for class org.intermine.web.struts.FindInListForm

Construct a new Form.

findLocationAndObjects(ObjectStore, Class<?>, Class<?>, boolean, boolean, boolean, int) - Static method in class org.intermine.bio.util.BioQueries

Query ObjectStore for all Location object between given object (eg.

findLockedPaths(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper

Get a list of paths that should not be removed from the query by the user.

findMostSpecificCommonTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

findMultipleCombinations(Set<Map<T, T>>) - Static method in class org.intermine.util.MappingUtil

Produces a Set of possible combinations of multiple mappings (as produced by findCombinations), where all mappings in a multiple mapping combination map onto distinct objects.

findNewQueryName(Set<String>) - Static method in class org.intermine.api.util.NameUtil

Return a query name that isn't currently in use.

findNewQueryName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil

Return a query name that isn't currently in use, returning the given name if it is available.

findParentPaths(String, PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper

Returns a List of paths, being the given path and all its parents.

findParticipatingLoops(LogicExpression, Map<PathConstraint, String>) - Static method in class org.intermine.api.query.MainHelper

Returns the Set of PathConstraintLoop objects that will participate in the QueryClass collapsing mechanism.

findProcessor(Class<? extends ChadoProcessor>) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Look at the list of completed processors and return the processor of the given type.

findResourcesMatching(Pattern) - Method in class org.intermine.web.struts.ResourceFinder

Find all resources matching a pattern in the WEB-INF directory.

findTableForAlias(String, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Finds a table in a Set with the given alias.

findTableNames(Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds a Set of all table names that are touched by a given query.

findTableNames(Query, DatabaseSchema, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Builds a Set of all table names that are touched by a given query.

finish() - Method in class org.intermine.util.ObjectPipe

Marks the ObjectPipe as finished - that is, no further Objects will be put into the ObjectPipe.

finishedItem(Item) - Method in class org.intermine.xml.full.FullHandler

Method that does something useful with the finished Item

finishedProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Perform any actions needed after all processing is finished.

finishedProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Perform any actions needed after all processing is finished.

fireEvent(OriginatingEvent) - Method in class org.intermine.api.profile.StorableBag

fireEvent(OriginatingEvent) - Method in interface org.intermine.api.search.WebSearchable

Notify all your observers of this event which originates at this web searchable.

fireEvent(OriginatingEvent) - Method in class org.intermine.api.template.ApiTemplate

first() - Method in class org.intermine.webservice.client.results.Page

Get the first page.

firstOrderByHasNoNulls - Variable in class org.intermine.sql.precompute.PrecomputedTable

firstPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Go to the first page

fixedEnumOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint

For an argument type which an enumerated value set, return the list of operators for which it makes sense only to provide the enumerated values and not allow the user to enter an arbitrary string.

fixEntityNames(String) - Static method in class org.intermine.util.XmlUtil

Replace greek character entity names with entity names that work in HTML.

fixFeatureType(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Fix types from the feature table, perhaps by changing non-SO type into their SO equivalent.

fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Convert ISO entities from FlyBase to HTML entities.

fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Process the identifier and return a "cleaned" version.

fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Process the identifier and return a "cleaned" version.

fixIdentifier(FeatureData, String, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Process the identifier and return a "cleaned" version.

fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor

Process the identifier and return a "cleaned" version.

fixInvalidBag(String, String) - Method in class org.intermine.api.profile.Profile

Fix this bag by changing its type

fixPubMedId(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Parser a pubmed id from a results string, extracted to a method so subclasses can override and fix prefixed pubmed ids.

fixPubMedId(String) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor

Wormbase chado has pmid prefixed to pubmed identifiers

fixUpForJoinStyle() - Method in class org.intermine.pathquery.PathQuery

Fixes up the order by list and the constraint logic, given the arrangement of outer joins in the query.

FLAT_FILES - Static variable in enum org.intermine.webservice.server.Format

Flat file formats: TSV, CSV

FlatFileFormatter - Class in org.intermine.webservice.server.output

A class to define behaviour common to flat files (csv, tsv)

FlatFileFormatter() - Constructor for class org.intermine.webservice.server.output.FlatFileFormatter

FlatFileWidgetResultProcessor - Class in org.intermine.webservice.server.widget

A widget result processor that produces results in flat file format (tsv/csv)

FlatListFormatter - Class in org.intermine.webservice.server.lists

Formats a list into its name.

FlatListFormatter() - Constructor for class org.intermine.webservice.server.lists.FlatListFormatter

FlatWidgetProcessor - Class in org.intermine.webservice.server.widget

FLOOR - Static variable in class org.intermine.objectstore.query.QueryFunction

Greatest integer value less than input.

flush() - Method in class org.intermine.dataloader.DataTracker

Flushes everything to the backing database.

flush() - Method in class org.intermine.sql.logging.DatabaseWriter

Flush completed rows to the database

flush() - Method in class org.intermine.sql.precompute.OptimiserCache

Removes all entries from the cache.

flush(Connection) - Method in class org.intermine.sql.writebatch.Batch

Flushes the batch out to the database server.

flush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch

Flushes the batch out to the database server.

flush() - Method in interface org.intermine.sql.writebatch.FlushJob

Performs the flush of all data represented by this object.

flush() - Method in class org.intermine.sql.writebatch.FlushJobBatchCommit

Performs the flush of all data represented by this object.

flush() - Method in class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl

Performs the flush of all data represented by this object.

flush() - Method in class org.intermine.sql.writebatch.FlushJobStatementBatchImpl

Performs the flush of all data represented by this object.

flush() - Method in class org.intermine.sql.writebatch.FlushJobUpdateStatistics

Performs the flush of all data represented by this object.

flush() - Method in class org.intermine.webservice.server.output.HTMLOutput

Prints html closing tags.

flush() - Method in class org.intermine.webservice.server.output.MemoryOutput

Does nothing because MemoryOutput serves as a storage of results during execution.

flush() - Method in class org.intermine.webservice.server.output.Output

Flushes output.

flush() - Method in class org.intermine.webservice.server.output.StreamedOutput

Finish writing.

FlushJob - Interface in org.intermine.sql.writebatch

An interface representing a job to be performed when actually flushing data to a database.

FlushJobBatchCommit - Class in org.intermine.sql.writebatch

A FlushJob that commits and re-opens a transaction on the database.

FlushJobBatchCommit(Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobBatchCommit

Constructor for this class

FlushJobPostgresCopyImpl - Class in org.intermine.sql.writebatch

An implementation of the FlushJob interface that represents a batch created in a Statement.

FlushJobPostgresCopyImpl(CopyManager, String, byte[], int) - Constructor for class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl

Constructor for this class

FlushJobStatementBatchImpl - Class in org.intermine.sql.writebatch

An implementation of the FlushJob interface that represents a batch created in a Statement.

FlushJobStatementBatchImpl(Statement) - Constructor for class org.intermine.sql.writebatch.FlushJobStatementBatchImpl

Constructor for this class

FlushJobUpdateStatistics - Class in org.intermine.sql.writebatch

An interface representing a job to be performed when actually flushing data to a database.

FlushJobUpdateStatistics(Map<String, Integer>, BatchWriter, Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobUpdateStatistics

Constructor for this class

flushLogTable() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Allows the log table to be flushed, guaranteeing that all log entries are committed to the database.

flushObjectById() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Completely empties the getObjectById cache.

flushObjectById() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Completely empties the getObjectById cache.

flushObjectById() - Method in interface org.intermine.objectstore.ObjectStore

Completely empties the getObjectById cache.

flushObjectById() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Completely empties the getObjectById cache.

flushObjectById() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Completely empties the getObjectById cache.

flushOldTempBagTables(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Removes any temporary bag tables that are no longer reachable.

FLYBASE_MISCELLANEOUS_CV - Static variable in class org.intermine.bio.dataconversion.FlyBaseProcessor

The cv.name for the FlyBase miscellaneous CV.

FLYBASE_SO_CV_NAME - Static variable in class org.intermine.bio.dataconversion.FlyBaseProcessor

The cv.name for the FlyBase miscellaneous CV.

FlyBaseCDSFastaLoaderTask - Class in org.intermine.bio.dataconversion

A fasta loader that understand the headers of FlyBase fasta CDS fasta files and can make the appropriate extra objects and references.

FlyBaseCDSFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask

FlyBaseFeatureFastaLoaderTask - Class in org.intermine.bio.dataconversion

Code for loading fasta for flybase, setting feature attribute from the FASTA header.

FlyBaseFeatureFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

FlyBaseIdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolver for Drosophila genes by querying tables in a FlyBase chado database.

FlyBaseIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Construct with class name/feature type to read from chado database or file.

FlyBaseIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Construct with class name/feature type to read from chado database or file.

FlyBaseIdResolverFactory(Set<String>) - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Construct with class name/feature type to read from chado database or file.

FlyBasePostProcess - Class in org.intermine.bio.postprocess

Copy transcript.introns to gene.introns.

FlyBasePostProcess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.FlyBasePostProcess

Create a new instance of FlyBasePostProcess

FlyBaseProcessor - Class in org.intermine.bio.dataconversion

A converter for chado that handles FlyBase specific configuration.

FlyBaseProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.FlyBaseProcessor

Create a new FlyBaseChadoDBConverter.

FlyBaseUniProtRefsTask - Class in org.intermine.bio.postprocess

Task to read a file mapping cds identifiers to UniProt accession numbers and create a protein reference in the CDSs.

FlyBaseUniProtRefsTask() - Constructor for class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

FlyBaseUTRFastaLoaderTask - Class in org.intermine.bio.dataconversion

A fasta loader that understand the headers of FlyBase fasta UTR fasta files and can make the appropriate extra objects and references.

FlyBaseUTRFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask

format(String) - Static method in class org.intermine.pathquery.ConstraintValueParser

Converts a Date to ISO date format.

format(List<? extends Object>) - Method in interface org.intermine.web.logic.export.RowFormatter

Format row to string.

format(List<? extends Object>) - Method in class org.intermine.web.logic.export.RowFormatterImpl

Formats objects to string.

format(double, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat

format(long, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat

Format - Enum in org.intermine.webservice.server

format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter

format(Job) - Method in interface org.intermine.webservice.server.idresolution.BagResultFormatter

Turn a job into a serialisable structure.

format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter

format(InterMineBag) - Method in class org.intermine.webservice.server.lists.FlatListFormatter

format(InterMineBag) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter

format(InterMineBag) - Method in class org.intermine.webservice.server.lists.JSONListFormatter

format(InterMineBag) - Method in interface org.intermine.webservice.server.lists.ListFormatter

Format a list into a list of string values.

format(PermanentToken) - Static method in class org.intermine.webservice.server.user.PermaTokens

Format a permanent token as a map.

FORMAT_PARAMETER_ANY - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

The parameter for accepting any format

FORMAT_PARAMETER_COUNT - Static variable in class org.intermine.webservice.client.core.RequestImpl

FORMAT_PARAMETER_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants comma separated output to be returned.

FORMAT_PARAMETER_CSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants comma separated output to be returned.

FORMAT_PARAMETER_HTML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants html output to be returned.

FORMAT_PARAMETER_JSON - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data

FORMAT_PARAMETER_JSON_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table

FORMAT_PARAMETER_JSON_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data in a data table

FORMAT_PARAMETER_JSON_OBJ - Static variable in class org.intermine.webservice.client.core.RequestImpl

FORMAT_PARAMETER_JSON_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data as nested objects representing records

FORMAT_PARAMETER_JSON_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table

FORMAT_PARAMETER_JSON_ROWS - Static variable in class org.intermine.webservice.client.core.RequestImpl

FORMAT_PARAMETER_JSON_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data suitable for using to construct tables with

FORMAT_PARAMETER_JSONP - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants jsonp data

FORMAT_PARAMETER_JSONP_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls

FORMAT_PARAMETER_JSONP_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants jsonp data in a data table

FORMAT_PARAMETER_JSONP_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data as above, but in a format suitable for cross site ajax calls

FORMAT_PARAMETER_JSONP_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls

FORMAT_PARAMETER_JSONP_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls

FORMAT_PARAMETER_TAB - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants tab separated output to be returned.

FORMAT_PARAMETER_TEXT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants plain text to be returned.

FORMAT_PARAMETER_TSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants tab separated output to be returned.

FORMAT_PARAMETER_XML - Static variable in class org.intermine.webservice.client.core.RequestImpl

FORMAT_PARAMETER_XML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Value of parameter when user wants xml output to be returned.

FORMAT_VERSION - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput

The version number of the database format

formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONFormatter

Format the header attributes.

formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONResultFormatter

This differs from the JSONFormatter implementation in that it will output a representation of all keys in the attributes map.

formatClass(ClassDescriptor, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Formats a class name, using the web-config to produce configured labels.

formatColumnName(String) - Static method in class org.intermine.web.logic.WebUtil

Formats column name.

formatExtraAttributes(Map<String, Map<String, Object>>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor

Format the value of extraAttribute.

formatField(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Format a path into a displayable field name.

formatField(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Format a path into a displayable field name.

formatFieldChain(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Format a sequence of fields in a chain.

formatFieldChain(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Format a path represented as a string to the formatted fields, without the class name.

formatFooter(String, int) - Method in class org.intermine.webservice.server.output.FlatFileFormatter

formatFooter(String, int) - Method in class org.intermine.webservice.server.output.Formatter

Returns formatted footer.

formatFooter(String, int) - Method in class org.intermine.webservice.server.output.JSONFormatter

Put on the final brace, and close the call-back bracket if needed.

formatFooter(String, int) - Method in class org.intermine.webservice.server.output.PlainFormatter

formatFooter(String, int) - Method in class org.intermine.webservice.server.output.XMLFormatter

formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter

Returns formatted header.

formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Formatter

Returns formatted header.

formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONFormatter

Add the opening brace, and a call-back if any

formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.PlainFormatter

formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.XMLFormatter

formatIsFlatFile() - Method in class org.intermine.webservice.server.WebService

formatIsJSON() - Method in class org.intermine.webservice.server.WebService

formatIsJsonObj() - Method in class org.intermine.webservice.server.query.AbstractQueryService

formatIsJSONP() - Method in class org.intermine.webservice.server.WebService

formatIsXML() - Method in class org.intermine.webservice.server.WebService

formatKVPair(String, Object) - Method in class org.intermine.pathquery.PathQuery

Format a key-value pair in a JSON compatible way.

formatPath(String, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil

Formats a column name, using the webconfig to produce configured labels.

formatPath(String, Model, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Formats a column name, using the webconfig to produce configured labels.

formatPath(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Formats a column name, using the webconfig to produce configured labels.

formatPath(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Formats a column name, using the given query to construct a path according to the current state of its subclasses.

formatPath(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Formats a column name, using the webconfig to produce configured labels.

formatPathDescription(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.

formatPathDescription(Path, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.

formatPathQueryView(PathQuery, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil

Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.

formatPathQueryView(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil

Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.Formatter

Returns formatted result item.

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONCountFormatter

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONFormatter

In normal cases a list with a single JSON string item is expected.

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.PlainFormatter

formatResult(List<String>) - Method in class org.intermine.webservice.server.output.XMLFormatter

Returns formatted result item.

formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchJSONProcessor

formatResult(KeywordSearchResult, boolean) - Method in interface org.intermine.webservice.server.search.QuickSearchResultProcessor

They take a results, and return one or more strings.

formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchTextProcessor

formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchXMLProcessor

formatResult(List<String>) - Method in class org.intermine.webservice.server.user.UserDataFormatter

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor

formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.EnrichmentResultProcessor

Format a row of results.

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphJSONProcessor

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphXMLProcessor

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableJSONProcessor

formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableXMLProcessor

formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.WidgetResultProcessor

Format a list of objects into a string representation.

FormattedTextParser - Class in org.intermine.util

Class for methods and util methods for parsing csv files and others.

Formatter - Class in org.intermine.webservice.server.output

Abstract class for formatting result data.

Formatter() - Constructor for class org.intermine.webservice.server.output.Formatter

formFile - Variable in class org.intermine.web.struts.ImportXMLForm

ForseenProblem - Exception in org.intermine.web.struts.oauth2

An exception type to plaster over the absence of first-class continuations in java.

ForseenProblem(String) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem

Construct one of these objects.

ForseenProblem(String, Object...) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem

Construct one of these objects.

forward() - Method in class org.intermine.web.struts.ForwardParameters

Construct the resulting ActionForward.

ForwardParameters - Class in org.intermine.web.struts

Utility wrapper class for programatically adding parameters to ActionForward paths.

ForwardParameters(ActionForward) - Constructor for class org.intermine.web.struts.ForwardParameters

Creates a new instance of ForwardParameters.

ForwardParameters(String, boolean) - Constructor for class org.intermine.web.struts.ForwardParameters

Creates a new instance of ForwardParameters with a given path and redirect settings.

friendlyMineManager - Variable in class org.intermine.api.InterMineAPI

FriendlyMineManager - Class in org.intermine.api.mines

Class to manage friendly mines

from - Variable in class org.intermine.sql.query.Query

FROM_DB - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

FromElement - Interface in org.intermine.objectstore.query

An element that can appear in the FROM clause of a query

full - Variable in class org.intermine.sql.precompute.BestQueryLogger

full - Variable in class org.intermine.task.AnalyseDbTask

FullHandler - Class in org.intermine.xml.full

Extension of DefaultHandler to handle parsing full XML.

FullHandler() - Constructor for class org.intermine.xml.full.FullHandler

Create a new FullHandler object.

FullParser - Class in org.intermine.xml.full

Unmarshal XML Full format data into java business objects.

FullRenderer - Class in org.intermine.xml.full

Render an object in InterMine Full XML format

FullXmlConverter - Class in org.intermine.dataconversion

Loads InterMine XML into an items database.

FullXmlConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FullXmlConverter

Constructor.

FullXmlConverterTask - Class in org.intermine.task

Load InterMine Items XML file(s) into a target items database.

FullXmlConverterTask() - Constructor for class org.intermine.task.FullXmlConverterTask

Function - Class in org.intermine.sql.query

A representation of a function in an SQL query.

Function(int) - Constructor for class org.intermine.sql.query.Function

Constructor for this Function object.

Function<A,B> - Interface in org.intermine.webservice.server.core

An interface for defining a thing that can take something and return something else.

G

GAFRecord - Class in org.intermine.bio.io.gaf

A record in a BED formatted file.

GAFRecord(String, int, int, String, int, String) - Constructor for class org.intermine.bio.io.gaf.GAFRecord

Constructor The following five attributes are normally hosted in InterMine cases.

GAFUtil - Class in org.intermine.bio.web.export

Utility methods for GAF format.

GeneInfoRecord - Class in org.intermine.bio.dataconversion

Data structure to hold information from one row of an NCBI Entrez gene_info file.

GeneInfoRecord(String, String, String, String, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.GeneInfoRecord

Construct information from file for one gene.

generate(WebserviceCodeGenInfo) - Method in interface org.intermine.api.query.codegen.WebserviceCodeGenerator

This method will generate web service source code from a path query or template query.

generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

This method will generate web service source code in Java from a path query or template query.

generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator

This method will generate code that can be run in a browser.

generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

This method will generate web service source code in Perl from a path query or template query.

generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

This method will generate code that will run using the python webservice client library.

generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

generate(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generate the output for a ClassDescriptor.

generate(AttributeDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generates code for a single attribute.

generate(ReferenceDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generates code for a single reference.

generate(CollectionDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generates code for a single collection.

generate(Query, int, int, DatabaseSchema, Database, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a Query object into an SQL String.

generate(Query, DatabaseSchema, Database, Constraint, int, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a Query object into an SQL String.

generate() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput

Generate a string that contains the torque data for the given schema.

generate(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput

Generate a string that describes the given ClassDescriptor.

generate24hrKey(Profile) - Method in class org.intermine.api.profile.ProfileManager

Generate a day token

generateAddCollectionElement(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the addCollectionElement method.

generateApiKey(Profile) - Method in class org.intermine.api.profile.ProfileManager

Generate a new API access key for this profile and return it.

generateApiKey(String) - Method in class org.intermine.dwr.AjaxServices

Generate a new API key for a given user.

generateCertificate(String, PublicKey) - Method in class org.intermine.web.security.KeySigner

Create a self-signed X.509 Certificate Should be eventually replaced with X509v3CertificateBuilder.

generateClassNames(String, Model) - Static method in class org.intermine.xml.full.ItemHelper

Generate a package qualified class name within the specified model from a space separated list of namespace qualified names

generateEquals(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generate a .equals() method for the given class.

generateFieldDescriptors(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generate all FieldDescriptors for a class/interface

generateGetElementType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the getElementType method.

generateGetFieldType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the getFieldType method.

generateGetFieldValue(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Generates the getFieldValue method.

generateGetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the getoBJECT method for producing NotXml.

generateGetSet(FieldDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput

Write code for getters and setters for given field.

generateHashCode(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generate a .hashCode() method for the given class.

generateIndirectionTable(CollectionDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput

Generate an indirection table

generateJdbcType(String) - Static method in class org.intermine.objectstore.intermine.TorqueModelOutput

Convert java primitive and object names to those compatible with torque.

generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.api.LinkRedirectManager

generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryListAppendService

generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService

Generate a list from a pathquery.

generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.template.TemplateListAppendService

generateNewName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil

Generate a new name for a list.

generatePassword() - Static method in class org.intermine.web.task.LoadDefaultTemplatesTask

Generate a random 8-letter String of lower-case characters

generatePermaLink(FastPathObject, String, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper

Generate a perma-link to a report page for an InterMine object.

generatePermaPath(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper

Generate a link suitable for use as an external, permanent link, in that the link should work between rebuilds of the database.

generatePortalLink(FastPathObject, InterMineAPI, HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper

Generate a stable link to a report page for the given object, this will create a portal link with the correct class and a value from a non-null class key field of the object.

generatePortalPath(FastPathObject, InterMineAPI) - Static method in class org.intermine.web.logic.PortalHelper

Generate an external portal link (perma-link) for an InterMine object.

generateQueryForId(Integer, Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Generates a query to retrieve a single object from the database, by id.

generateRandomUniqueString() - Static method in class org.intermine.api.util.TextUtil

generateRandomUniqueString(int) - Static method in class org.intermine.api.util.TextUtil

generateReadOnlyAccessToken(Profile, String) - Method in class org.intermine.api.profile.ProfileManager

Return a permanent user access token, with ReadOnly permission.

generateReportLink(ResultElement, String) - Static method in class org.intermine.web.logic.PortalHelper

Generate a link to the object details page using the internal id.

generateReportPath(ResultCell) - Static method in class org.intermine.web.logic.PortalHelper

Get the path fragment (starting with "/") for the report page for an object in the mine.

generateSetFieldValue(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the setFieldValue method.

generateSetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generates the setoBJECT method for deserialising objects.

generateSingleUseKey(Profile) - Method in class org.intermine.api.profile.ProfileManager

Generate a single use API key and store it in memory, before returning it.

generateSql(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Generate sql from a Query

generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().

generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().

generateSqlCompatibleName(String) - Static method in class org.intermine.sql.DatabaseUtil

Convert any sql keywords to valid names for tables/columns.

generateToString(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Generate a .toString() method for the given class .

generationSqlString - Variable in class org.intermine.sql.precompute.PrecomputedTable

geneType - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

GenomeDBConverter - Class in org.intermine.bio.dataconversion

A ChadoDBConverter that sets the dataset and datasource for genome databases (eg.

GenomeDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.GenomeDBConverter

Create a new ChadoDBConverter object.

get(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

get(int) - Method in class org.intermine.api.results.WebResults

get(int) - Method in class org.intermine.objectstore.query.Results

get(Object) - Method in class org.intermine.util.AlwaysMap

get(Object) - Method in class org.intermine.util.IdentityMap

get(int) - Method in class org.intermine.util.IntToIntMap

Retrieves a mapping from the object

get(Integer) - Method in class org.intermine.util.IntToIntMap

Retrieves a mapping from the object.

get(Object) - Method in class org.intermine.util.ReferenceMap

get(Path, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory

Get a display constraint.

get(PathConstraint, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory

Get a display constraint.

get(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory

Get a ReportObject for the given InterMineObject.

get(String) - Method in class org.intermine.web.security.KeyStorePublicKeySource

get(String) - Method in interface org.intermine.web.security.PublicKeySource

Get a specific key by name.

get(int) - Method in class org.intermine.webservice.client.lists.ItemList

Get an item by its index.

get(int) - Method in class org.intermine.webservice.client.results.JsonRow

get(Object) - Method in class org.intermine.webservice.client.results.JsonRowMap

get(int) - Method in class org.intermine.webservice.client.results.ResultRowList

get(Object) - Method in class org.intermine.webservice.client.results.ResultRowMap

getAbbreviation() - Method in class org.intermine.bio.util.OrganismData

Get the abbreviation of this organism.

getAbbreviation(String) - Static method in class org.intermine.webservice.server.CodeTranslator

Returns corresponding abbreviation of translated operation.

getAcceptableFormats(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser

Get the list of formats that this request finds acceptable.

getAccepted() - Method in class org.intermine.api.bag.SharingInvite

getAccepted() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite

getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getAccessCounter(Connection) - Method in class org.intermine.api.tracker.TemplateTracker

Return the number of executions for each public template

getAccessCounter() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the rank associated to the templates

getAccessibleLists() - Method in class org.intermine.webservice.client.services.ListService

Returns all the lists that this service has access to.

getAccessions() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getAction() - Method in class org.intermine.api.search.TaggingEvent

getAction() - Method in class org.intermine.web.struts.WidgetForm

getActionMessage(String, int, String, String) - Method in class org.intermine.web.logic.bag.BagConverter

Get the ActionMessage to display in the webapp

getActionMessage() - Method in exception org.intermine.web.struts.oauth2.ForseenProblem

Get a struts action message, rather than a simple string message.

getActionType() - Method in class org.intermine.web.struts.TemplateSettingsForm

getAddIssues() - Method in class org.intermine.webservice.server.lists.ListCreationInput

getAdditionalBeanInfo() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getAdditionalBeanInfo() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getAdditionalConverters(String) - Method in class org.intermine.api.bag.BagQueryConfig

Return a Map from a converter Class name (such as org.intermine.bio.web.logic.OrthologueConverter) to set of additional converters.

getAdditionalFields() - Method in class org.intermine.web.search.KeywordSearchResult

additional display field expressions

getAdditionalParameter(HttpServletRequest, String) - Static method in class org.intermine.web.logic.PortalHelper

Searches a request for additional parameters that might match an additional converter.

getAlgorithm() - Method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy

getAlias() - Method in class org.intermine.sql.query.AbstractTable

Returns the alias for this AbstractTable object.

getAlias() - Method in class org.intermine.sql.query.SelectValue

Gets the alias from this object.

getAliasedColumnHeaders(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Get the view for a path query reformatted to obey the labels given in webconfig.

getAliases() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return all values of the Alias field from the attributes of this record.

getAliases() - Method in class org.intermine.objectstore.query.Query

Returns the map of QuerySelectables and FromElements to String aliases

getAll() - Method in class org.intermine.web.security.KeyStorePublicKeySource

getAll() - Method in interface org.intermine.web.security.PublicKeySource

getAllBags() - Method in class org.intermine.api.profile.Profile

Get all bags associated with this profile, both valid and invalid.

getAllChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm

Return a Set of all the child ChadoCVTerms of this term.

getAllClassDescriptors() - Method in class org.intermine.xml.full.Item

Return the ClassDescriptors of the class of this Item (as given by className) and all the implementations.

getAllCVTerms() - Method in class org.intermine.bio.chado.ChadoCV

Return a Set of all the CVTerms in this CV.

getAlleleCVTermsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Get result set of feature_id, cvterm_id pairs for the alleles in flybase chado.

getAllelePropPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing the featureprop_id and the publication identifier of the featureprops for al alleles.

getAllelePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing the alleles and their featureprops.

getAllJSONResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Returns all the results for the given template template, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).

getAllJSONResults(String) - Method in class org.intermine.webservice.client.services.QueryService

Fetch all the results as a list of JSON Objects

getAllJSONResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Returns all the results for the given template template with the given parameters, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).

getAllNullAttributes() - Method in class org.intermine.objectstore.ObjectStoreSummary

Get a list of the attributes that are always null or empty.

getAllNullReferencesAndCollections() - Method in class org.intermine.objectstore.ObjectStoreSummary

Get a list of reference and collection names that are always null or empty.

getAllParents() - Method in class org.intermine.bio.chado.ChadoCVTerm

Return a Set of all the parent ChadoCVTerms of this term.

getAllParents() - Method in class org.intermine.bio.postprocess.PopulateChildFeatures

getAllPartOfs(String) - Method in class org.intermine.bio.ontology.SequenceOntology

getAllReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager

Get all displayers for the given type regardless of placement.

getAllResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Returns all the results for the given template template.

getAllResults(String) - Method in class org.intermine.webservice.client.services.QueryService

Returns all of the results of the specified PathQuery.

getAllResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Returns all the results for the given template template with the given parameters.

getAllRowIterator(String) - Method in class org.intermine.webservice.client.services.QueryService

Returns all the results of a specified PathQuery as an iterator.

getAllRows() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return all the resultElementRows of the table as a List of Lists.

getAllRowsIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Returns an iterator over all the rows for the template.

getAllRowsIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Returns all the rows for the template when run with the given parameters.

getAllSelected() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getAllSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

If a whole column is selected, return its index, otherwise return -1.

getAllSuperUsers() - Method in class org.intermine.api.profile.ProfileManager

getAlteredViews(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj

Get the views for the transformed query.

getAnalysedTotal() - Method in class org.intermine.web.logic.widget.EnrichmentResults

Get the number of items in the sample that had an attribute value.

getAnnotatedCountsInPopulation() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

For each attribute give a count of items in the whole population that have that attribute assigned to them, M.

getAnnotatedCountsInPopulation() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getAnnotatedCountsInSample() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

For each attribute give a count of items in the sample that have that attribute assigned to them, k.

getAnnotatedCountsInSample() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getApiKey() - Method in class org.intermine.api.profile.Profile

getAPIVersion() - Method in class org.intermine.webservice.client.core.Service

getAppendConfig() - Method in class org.intermine.web.logic.config.HeaderConfigTitle

getApplicationName() - Method in class org.intermine.webservice.client.core.Service

getAppliedData(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for data from the applied_protocol_data table.

getAppliedDataAll(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for data from the applied_protocol_data table.

getAppliedDataAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Query to get data attributes.

getAppliedDataCharacteristics(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for data from the applied_protocol_data table.

getAppliedProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed from the appliedProtocol table.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryCast

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in interface org.intermine.objectstore.query.QueryEvaluable

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryExpression

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryField

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryForeignKey

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryFunction

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.QueryValue

Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.

getApproximateType() - Method in class org.intermine.objectstore.query.UnknownTypeValue

Returns the approximate type of the argument.

getArg1() - Method in class org.intermine.objectstore.query.ClassConstraint

Returns the QueryClass argument 1

getArg1() - Method in class org.intermine.objectstore.query.QueryExpression

Returns the left argument of the expression.

getArg1() - Method in class org.intermine.objectstore.query.SimpleConstraint

Returns the left argument of the constraint.

getArg2() - Method in class org.intermine.objectstore.query.QueryExpression

Returns the right argument, or the position argument of the substring.

getArg2() - Method in class org.intermine.objectstore.query.SimpleConstraint

Returns the right argument of the constraint.

getArg2Object() - Method in class org.intermine.objectstore.query.ClassConstraint

Returns the Object argument 2

getArg2QueryClass() - Method in class org.intermine.objectstore.query.ClassConstraint

Returns the QueryClass argument 2

getArg3() - Method in class org.intermine.objectstore.query.QueryExpression

Returns the length argument of a substring expression.

getAspect(String) - Static method in class org.intermine.api.tag.AspectTagUtil

Extracts aspect from tag name.

getAspectDisplayers() - Method in class org.intermine.web.logic.config.Type

getAspects() - Method in class org.intermine.web.logic.config.Displayer

Get the aspects of this displayer

getAspects(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns the Map of aspects.

getAspectSources() - Method in class org.intermine.web.logic.aspects.Aspect

Get the AspectSources.

getAspectTemplates(String) - Method in class org.intermine.api.template.TemplateManager

Get public templates for a particular aspect.

getAspectTemplates(String, Integer) - Method in class org.intermine.api.template.TemplateManager

Get public templates for a particular aspect.

getAttribute() - Method in class org.intermine.bio.dataconversion.UniprotEntry

the identifier is only held until the next line of the XML is processed, at which point the item is stored

getAttribute(String) - Static method in class org.intermine.web.context.InterMineContext

Get the value of a stored attribute.

getAttribute(String) - Method in class org.intermine.xml.full.Item

Get a named attribute.

GetAttributeAsFileAction - Class in org.intermine.web.struts

Provide an attribute value as a file

GetAttributeAsFileAction() - Constructor for class org.intermine.web.struts.GetAttributeAsFileAction

getAttributeDescriptors() - Method in class org.intermine.web.logic.results.ReportObject

Get attribute descriptors.

getAttributeIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask

Add indexes for all fields to the relevant tables for a given ClassDescriptor.

getAttributeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of attributeOp

getAttributeOps() - Method in class org.intermine.web.struts.TemplateForm

Get the attribute ops

getAttributeOps(String) - Method in class org.intermine.web.struts.TemplateForm

Get an attribute op

getAttributeOptions() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of attributeValue

getAttributes() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the attributes of this record as a Map from attribute key to Lists of attribute values.

getAttributes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields

Returns the Set of attributes

getAttributes() - Method in class org.intermine.web.logic.results.ReportObject

Get the attribute fields and values for this object

getAttributes() - Method in class org.intermine.xml.full.Item

Get all the attributes.

getAttributesFromBag(InterMineBag, ObjectStore, String, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper

getAttributesFromBag(InterMineBag, ObjectStore, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper

Used by esyn tool

getAttributeValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of attributeValue

getAttributeValues() - Method in class org.intermine.web.struts.TemplateForm

Get the attribute values

getAttributeValues(String) - Method in class org.intermine.web.struts.TemplateForm

Get an attribute value

getAuthenticatedUser() - Method in class org.intermine.webservice.server.WebService

Get a profile that is a true authenticated user that exists in the database.

getAutoCompleter() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the autocompleter for this path if one is available.

getAutoCompleter(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the AutoCompleter stored on the ServletContext.

getAverage() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary

getBag(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch a global or user or shared bag by name.

getBag() - Method in class org.intermine.api.bag.SharingInvite

getBag() - Method in class org.intermine.objectstore.query.BagConstraint

Get the bag Collection.

getBag() - Method in interface org.intermine.objectstore.query.ConstraintWithBag

Returns the bag that the constraint is using.

getBag() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint

Returns the bag that this object was constructed with.

getBag() - Method in class org.intermine.objectstore.query.QueryClassBag

Returns the bag of objects.

getBag() - Method in class org.intermine.pathquery.PathConstraintBag

Returns the bag name that the constraint is constraining to.

getBag() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

the bag that this widget is using

getBag(String) - Method in class org.intermine.web.struts.TemplateForm

Get the bag name selected.

getBagConverter(InterMineAPI, WebConfig, String) - Static method in class org.intermine.web.logic.PortalHelper

Returns a BagConverter for the given parameters.

getBagCreationQuery() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return a Query that produces a Results object of the selected objects.

getBagDisplayers() - Method in class org.intermine.web.logic.config.Type

Get the List of bag Displayers

getBagId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getBagId() - Method in class org.intermine.objectstore.query.ObjectStoreBag

Returns the identifier of the bag.

getBagManager() - Method in interface org.intermine.api.API

getBagManager() - Method in class org.intermine.api.InterMineAPI

getBagManager() - Static method in class org.intermine.api.query.PathQueryAPI

Returns a BagManager.

getBagName() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

getBagName() - Method in class org.intermine.web.struts.FindInListForm

getBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Get the value of bagName

getBagName() - Method in class org.intermine.web.struts.WidgetForm

getBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

Get the type of the bag

getBagNames() - Method in class org.intermine.pathquery.PathQuery

Returns all bag names used in constraints on this query.

getBagOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of bagOp

getBagOp(String) - Method in class org.intermine.web.struts.TemplateForm

Get the bag operation selected.

getBagOps() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the valid constraint ops when constraining on a bag.

getBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig

Return a list of BagQuerys to run for a given type

getBagQueries() - Method in class org.intermine.api.bag.BagQueryHandler

Return the bag queries from the XML file.

getBagQueryConfig() - Method in interface org.intermine.api.API

getBagQueryConfig() - Method in class org.intermine.api.bag.BagQueryHandler

Return the BagQueryConfig created from the XML.

getBagQueryConfig() - Method in class org.intermine.api.InterMineAPI

getBagQueryConfig() - Static method in class org.intermine.api.query.PathQueryAPI

Returns a BagQueryConfig configured in WEB-INF/bag-queries.xml.

getBagQueryResult() - Method in class org.intermine.api.bag.BagQueryUpgrade

getBagQueryRunner() - Method in interface org.intermine.api.API

getBagQueryRunner() - Method in class org.intermine.api.InterMineAPI

The bag-query runner is the object that performs look-up queries used when constructing bags from lists of identifiers, and in path-queries when LOOKUP constraints are used.

getBags(Profile) - Method in class org.intermine.api.bag.BagManager

Fetch all global bags, user bags and shared bags combined in the same map.

getBags() - Method in class org.intermine.api.bag.operations.BagOperation

getBags() - Method in class org.intermine.api.profile.BagSet

getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

Returns the List of bags.

getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject

Returns the Collection of bags.

getBags() - Method in class org.intermine.web.logic.query.DisplayConstraint

Get a list of public and user bag names available and currentfor this path.

getBagsAndClasses(Set<ClassDescriptor>, Set<InterMineBag>, Profile, BagManager, Model, String[]) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils

Given an array of bag names, populate both a set of bags, and a set of class-descriptors with the objects these names refer to.

getBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch global and user bags of the specified type or a subclass of the specified type.

getBagsOfType(Profile, String, boolean) - Method in class org.intermine.api.bag.BagManager

Fetch global and user bags of the specified type or a subclass of the specified type.

getBagTableNames() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getBagType() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the bag type that the constraint can be constrained to.

getBagType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getBagType() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Get the bag type - hidden form value.

getBagType() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

getBagType() - Method in class org.intermine.web.struts.WidgetForm

getBagValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of bagValue

getBaseEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Returns the base equivalent object fetcher.

getBaseLink() - Method in class org.intermine.web.tags.table.NavigationBarTag

getBaseUrl() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getBaseUrl(HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper

Get the base url for this web-app.

getBaseURL() - Method in class org.intermine.web.util.AttributeLinkURL

getBaseURL() - Method in class org.intermine.web.util.URLGenerator

getBatch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Gets a batch by whatever means - maybe batches, maybe the ObjectStore.

getBatchFromCache(int) - Method in class org.intermine.objectstore.query.ResultsBatches

Returns the given batch, if it is already in the batch cache.

getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.Results

Gets the batch for a particular row

getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.ResultsBatches

Gets the batch for a particular row

getBatchSize() - Method in class org.intermine.objectstore.query.Results

Gets the batch size being used.

getBatchSize() - Method in class org.intermine.objectstore.query.ResultsBatches

Gets the batch size being used.

getBeanDescriptor() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getBeanDescriptor() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getBest() - Method in class org.intermine.sql.precompute.BestQueryExplainer

Gets the best Candidate found so far.

getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryExplainer

Gets the ExpainResult for the best Query found so far.

getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryFallback

Gets the ExpainResult for the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.BestQuery

Gets the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer

Gets the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryFallback

Gets the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryLogger

Gets the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryStorer

Gets the best Query found so far

getBestQuery() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery

Gets the best Query found so far

getBestQueryString() - Method in class org.intermine.sql.precompute.BestQuery

Gets the best query String found so far

getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer

Gets the best query String found so far.

getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryFallback

Gets the best query String found so far

getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryLogger

Gets the best query String found so far

getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryStorer

Gets the best query String found so far

getBestQueryString() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery

Gets the best query String found so far

getBgcolor() - Method in class org.intermine.api.mines.LocalMine

getBgcolor() - Method in interface org.intermine.api.mines.Mine

getBgcolor() - Method in class org.intermine.api.mines.RemoteMine

getBinaryIndexMap() - Method in class org.intermine.web.autocompletion.AutoCompleter

Returns byte array of the RAMIndexMap

getBinsParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction

getBlockCount() - Method in class org.intermine.bio.io.bed.BEDRecord

getBlockCount() - Method in class org.intermine.bio.io.gaf.GAFRecord

getBlockSizes() - Method in class org.intermine.bio.io.bed.BEDRecord

getBlockSizes() - Method in class org.intermine.bio.io.gaf.GAFRecord

getBlockStarts() - Method in class org.intermine.bio.io.bed.BEDRecord

getBlockStarts() - Method in class org.intermine.bio.io.gaf.GAFRecord

getBoolean(String) - Method in class org.intermine.webservice.client.results.Item

Get a property known to be an boolean.

getBuffer() - Method in class org.intermine.sql.writebatch.PostgresByteArrayOutputStream

Returns the byte buffer without copying it.

getBuildMode() - Method in class org.intermine.api.tracker.track.ListTrack

Return the way the list is built

getButton() - Method in class org.intermine.web.logic.query.MetadataNode

Gets the value of button

getByChadoId(Integer) - Method in class org.intermine.bio.chado.ChadoCV

Return the ChadoCVTerm object for a given cvterm_id.

getByToken(InterMineAPI, String) - Static method in class org.intermine.api.bag.SharingInvite

getCallback() - Method in class org.intermine.webservice.server.WebService

Get the value of the callback parameter.

getCanCreateConstraint() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if there is any possibility of creating a constraint on this path.

getCandidateLoops(String) - Method in class org.intermine.pathquery.PathQuery

Returns the set of paths that could feasibly be loop constrained onto the given path, given the current outer join situation.

getCandidateLoops() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the set of paths that could feasibly be loop constrained onto the constraint's path, given the query's outer join situation.

getCaseSensitive() - Method in interface org.intermine.api.idresolution.JobInput

getCaseSensitive() - Method in class org.intermine.web.logic.bag.WebJobInput

getCaseSensitive() - Method in class org.intermine.web.struts.BuildBagForm

getCategories(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Gets the aspect categories from the servlet context.

getCategory() - Method in class org.intermine.sql.precompute.PrecomputedTable

Returns the category of this PrecomputedTable

getCategoryPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getCauseElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getCauseElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getCDNALengthResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing the feature_id and its seqlen The method is protected so that is can be overridden for testing.

getChadoCV(String) - Method in class org.intermine.bio.chado.ChadoCVFactory

Get a new ChadoCV containing only cv terms from the cv with the given name.

getChadoDBConverter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Return the ChadoDBConverter that was passed to the constructor.

getChadoIdToOrgDataMap() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Return a map from chado organism_id to OrganismData object for all the organisms that we are processing

getChadoOrganismIds(Connection) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Return a map from chado organism id to OrganismData for the organisms in the organism table in chado.

getCharSet() - Method in class org.intermine.webservice.client.core.ContentType

getChartType() - Method in class org.intermine.webservice.client.widget.Widget

getChartWidgets() - Method in class org.intermine.webservice.client.services.WidgetService

getChildId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Get childId value

getChildren() - Method in class org.intermine.pathquery.LogicExpression.Operator

Get an unmodifiable copy of the node's children.

getChildren(ClassDescriptor) - Static method in class org.intermine.web.struts.InitialiserPlugin

Get the names of the type of this ClassDescriptor and all its descendants

getChildren(ClassDescriptor, Set<String>) - Static method in class org.intermine.web.struts.InitialiserPlugin

Add the names of the descendents of a ClassDescriptor to a Set

getChildTermId() - Method in class org.intermine.bio.ontology.OboRelation

getChrom() - Method in class org.intermine.bio.io.bed.BEDRecord

getChrom() - Method in class org.intermine.bio.io.gaf.GAFRecord

getChromEnd() - Method in class org.intermine.bio.io.bed.BEDRecord

getChromEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord

getChromosome(String, int) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Make a Chromosome Item, then store and return it.

getChromosome(String, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Return a Chromosome object for the given item.

getChromosomeFeatureMap(Integer) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Fetch the populated map of chromosome-like features.

getChromosomeFeatureTypes() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Get a list of the chado/so types of the Chromosome-like objects we wish to load.

getChromosomeStructureVariationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return the results of running a query for the chromosome_structure_variation feature types.

getChromStart() - Method in class org.intermine.bio.io.bed.BEDRecord

getChromStart() - Method in class org.intermine.bio.io.gaf.GAFRecord

getClassConfig() - Method in class org.intermine.web.logic.config.FieldConfig

getClassCount(String) - Method in class org.intermine.objectstore.ObjectStoreSummary

Get the number of instances of a particular class in the ObjectStore.

getClassDescriptor() - Method in class org.intermine.web.logic.results.ReportObject

Get the class descriptor for this object

getClassDescriptorByName(String) - Method in class org.intermine.xml.full.Item

Throw a RuntimeException if any of the named class isn't in the Model set by setModel().

getClassDescriptors() - Method in class org.intermine.api.profile.InterMineBag

Return the class descriptors for the type of this bag.

getClasses() - Method in class org.intermine.api.bag.operations.BagOperation

getClassesForBags(Collection<InterMineBag>) - Method in class org.intermine.webservice.server.lists.AbstractListService

Get the classes represented by a collection of bags.

getClassFieldConfigs(WebConfig, ClassDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper

Find the FieldConfig objects for the the given ClassDescriptor (or generate them).

getClassFieldConfigs(ClassDescriptor) - Method in class org.intermine.web.logic.results.InlineResultsTable

Find the FieldConfig objects for the the given ClassDescriptor.

getClassIndex(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper

getClassIndexes(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper

getClassKeys() - Method in interface org.intermine.api.API

getClassKeys() - Method in class org.intermine.api.bag.operations.BagOperation

getClassKeys() - Method in class org.intermine.api.InterMineAPI

The class keys are the list of fields used to identify objects in the data base, so for Employee it would include "name", and for Gene it would include "symbol".

getClassKeys() - Static method in class org.intermine.api.query.PathQueryAPI

Returns classkeys configured in class_keys.properties.

getClassKeys() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

Get the classKeys

getClassName() - Method in class org.intermine.api.bag.AdditionalConverter

getClassName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction

Return the className that was passed to the constructor.

getClassName() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Return the class name set with setClassName().

getClassName() - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getClassName

getClassName() - Method in class org.intermine.web.logic.config.TableExportConfig

Get the class name of the exporter eg. org.intermine.bio.web.export.SequenceHttpExporter

getClassName() - Method in class org.intermine.web.logic.config.Type

Get the class name

getClassName() - Method in class org.intermine.web.logic.results.InlineResultsTableRow

getClassName() - Method in class org.intermine.web.logic.results.InlineTableResultElement

getClassName() - Method in class org.intermine.web.struts.QueryClassSelectForm

Get the class name

getClassName() - Method in class org.intermine.xml.full.Item

Get the class name of this item.

getClassName(Object, Model) - Static method in class org.intermine.xml.XmlHelper

Get the class name if object represents a material class in model.

getClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver

Return a set of class names the reslover holds

getClassNames(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Given a String, perform a one of a set of expansions and return a Set of unqualified class names.

getClazz() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass

Returns the class.

getClientId() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getClientId() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getClientId() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getClientSecret() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getClientSecret() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getClientSecret() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getClob() - Method in class org.intermine.objectstore.query.ClobAccess

Return the Clob that this object is accessing.

getClob() - Method in class org.intermine.objectstore.query.PendingClob

Return the Clob that this object is accessing.

getClobId() - Method in class org.intermine.objectstore.query.Clob

Returns the identifier of the Clob.

getCode() - Method in class org.intermine.web.logic.query.DisplayConstraint

If editing an existing constraint get the code for this constraint in the query, return null if creating a new constraint.

getCode() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Get the code associated with this constraint in the query.

getCode() - Method in class org.intermine.web.logic.template.ConstraintInput

getCode() - Method in class org.intermine.webservice.client.template.TemplateParameter

getCode(String) - Static method in class org.intermine.webservice.server.CodeTranslator

Returns corresponding code of translated operation.

getCode() - Method in class org.intermine.webservice.server.output.Output

Gets the error code

getCollection() - Method in class org.intermine.web.logic.results.DisplayCollection

getCollection() - Method in class org.intermine.web.logic.results.ReportInList

getCollection(String) - Method in class org.intermine.webservice.client.results.Item

Get a set of items representing the elements in a collection field on an item.

getCollection(String) - Method in class org.intermine.xml.full.Item

Get a named collection.

getCollections() - Method in class org.intermine.web.logic.results.ReportObject

Get the collection fields and values for this object

getCollections() - Method in class org.intermine.xml.full.Item

Get all the collections.

getColNames() - Method in class org.intermine.sql.writebatch.TableBatch

Returns the column names.

getColumn() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary

getColumnAliases(Query) - Static method in class org.intermine.objectstore.query.QueryHelper

Returns a list of aliases, where each alias corresponds to each element of the SELECT list of the Query object.

getColumnClasses(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper

getColumnFieldClasses() - Method in class org.intermine.task.DelimitedFileConfiguration

Return a List of Class objects corresponding to the fields returned by getColumnFieldDescriptors().

getColumnFieldDescriptors() - Method in class org.intermine.task.DelimitedFileConfiguration

Return a List of the configured AttributeDescriptors.

getColumnHeaders() - Method in class org.intermine.pathquery.PathQuery

Returns the paths descriptions for the view.

getColumnHeaderStyle() - Method in class org.intermine.webservice.server.WebService

Get an enum which represents the column header style (path, friendly, or none)

getColumnId() - Method in class org.intermine.api.results.Column

getColumnIdentifier() - Method in class org.intermine.api.results.Column

Used in the view to match this element

getColumnName(FieldDescriptor) - Static method in class org.intermine.sql.DatabaseUtil

Creates a column name for a field descriptor

getColumnNames() - Method in class org.intermine.api.results.WebResults

Return the names of the columns of the results.

getColumnNames() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the column names

getColumnNames() - Method in class org.intermine.web.tags.table.TableTag

getColumnPaths(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper

Return a List containing the Path objects from the Columns of this PagedTable.

getColumns() - Method in class org.intermine.api.results.ExportResultsIterator

Allows test to access column info.

getColumns() - Method in class org.intermine.api.results.WebResults

Returns the columns for these results.

getColumns() - Method in interface org.intermine.api.results.WebTable

Returns the Column objects for this table.

getColumns() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the list of column configurations

getColumns() - Method in class org.intermine.web.logic.widget.TableWidget

Get the columns

getColumns() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

Get the columnNames

getColumns() - Method in class org.intermine.webservice.server.core.SubTable

getColumnsPath() - Method in class org.intermine.api.results.WebResults

getColumnsPath() - Method in interface org.intermine.api.results.WebTable

getColumnsSize() - Method in class org.intermine.web.logic.results.InlineResultsTable

getColumnSummary(String, String) - Static method in class org.intermine.dwr.AjaxServices

Get the summary for the given column

getColumnTitle() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getColumnTypes(Query) - Static method in class org.intermine.objectstore.query.QueryHelper

Returns a list of Class objects, where each object corresponds to the type of each element of the SELECT list of the Query object.

getColumnTypeString(Class<?>) - Method in class org.intermine.sql.Database

Return the SQL type used to store objects of the given Class.

getComment() - Method in class org.intermine.template.TemplateQuery

Get the private comment for this template.

getComment() - Method in class org.intermine.web.struts.TemplateSettingsForm

Return the comment

getCommentEvidence() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getComments() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getCommentType() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getCommonFeaturesMap() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Get a map of features that are expected to be common between submissions.

getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery

Get the JSON prefix common to all constraints.

getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.template.TemplateQuery

getCompatibleCurrentBags(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch global and user bags current of the specified type or a subclass or any superclass of the specified type.

getComplete() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns the estimated amount of time taken to produce the entire set of results.

getComplete() - Method in class org.intermine.sql.query.ExplainResult

Returns the number of page requests before the query is completed, estimated by the database for this query.

getCompletedProcessors() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

getComponents() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getComponentsForQuery(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Returns a Set of independent components that affect the results of the given Query.

getComponentsForQuery(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns a Set of independent components that affect the results of the given Query.

getComponentsForQuery(Query) - Method in interface org.intermine.objectstore.ObjectStore

Returns a Set of independent components that affect the results of the given Query.

getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Returns a Set of independent components that affect the results of the given Query.

getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Returns a Set of independent components that affect the results of the given Query.

getComponentsForQuery(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Returns a Set of independent components that affect the results of the given Query.

getConfig(int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return the config Map.

getConfig(int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Return the config Map.

getConfig(int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the config Map.

getConfig(int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor

Return the config Map.

getConfig(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory

Return the TableExportConfig for the given id.

getConfigClassDescriptor() - Method in class org.intermine.task.DelimitedFileConfiguration

Return the ClassDescriptor of the class to modify.

getConfigId() - Method in class org.intermine.web.logic.widget.Widget

Get the ID of the corresponding WidgetConfig

getConfiguredTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the unqualified class names for which this displayer should be displayed.

getConnectField() - Method in class org.intermine.api.bag.BagQueryConfig

Return the connecting field.

getConnection() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Get the connection to use when processing.

getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns a Connection.

getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Returns a Connection.

getConnection() - Method in class org.intermine.sql.Database

Gets a Connection to this Database

getConstrainField() - Method in class org.intermine.api.bag.BagQueryConfig

Return the constrain field.

getConstraint() - Method in class org.intermine.objectstore.query.Query

Get the current constraint on this Query

getConstraint() - Method in interface org.intermine.objectstore.query.Queryable

Returns the additional constraint.

getConstraint() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the additional constraint.

getConstraint() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the additional constraint.

getConstraint() - Method in class org.intermine.sql.query.NotConstraint

Returns the contained constraint.

getConstraint() - Method in class org.intermine.template.TemplateValue

Returns the constraint that this object was constructed with.

getConstraintCodes() - Method in class org.intermine.pathquery.PathQuery

Return the constraint codes used in the query, some constraint types (subclasses) don't get assigned a code, these are not included.

getConstraintDescription(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Returns the description attached to the given constraint.

getConstraintDescriptions() - Method in class org.intermine.template.TemplateQuery

Returns the constraint descriptions for this query.

getConstraintForCode(String) - Method in class org.intermine.pathquery.PathQuery

Returns the PathConstraint associated with a given code.

getConstraintGroups() - Method in class org.intermine.pathquery.PathQuery

Returns the outer join constraint codes groups map for this query, if the query verifies correctly.

getConstraintLogic() - Static method in class org.intermine.dwr.AjaxServices

Get the grouped constraint logic

getConstraintLogic() - Method in class org.intermine.pathquery.PathQuery

Returns the current constraint logic.

getConstraintLogicForEditableConstraints() - Method in class org.intermine.template.TemplateQuery

Return the constraint logic modified to contain only the blocks with editable constraints

getConstraintLogicForGroup(String) - Method in class org.intermine.pathquery.PathQuery

Returns the constraint logic for the given outer join group, if the query verifies correctly.

getConstraintOp() - Method in class org.intermine.web.logic.template.ConstraintInput

Returns constraint operation

getConstraintPath() - Method in class org.intermine.api.bag.AdditionalConverter

getConstraints() - Method in class org.intermine.objectstore.query.ConstraintSet

Returns the Set of constraints.

getConstraints() - Method in class org.intermine.pathquery.PathQuery

Returns a Map of all the constraints in this query, from PathConstraint to the constraint code used in the constraint logic.

getConstraints() - Method in class org.intermine.sql.query.ConstraintSet

Returns the Set of constraints forming this object.

getConstraints() - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Return summary representations of constraints on this path or an empty list if none exist.

getConstraints() - Method in class org.intermine.web.logic.template.TemplateResultInput

Returns constraints.

getConstraintsForPath(String) - Method in class org.intermine.pathquery.PathQuery

Returns a list of PathConstraints applied to a given path or an empty list.

getConstraintSwitchOffAbility() - Method in class org.intermine.template.TemplateQuery

Returns the constraint SwitchOffAbility for this query.

getContainsOptions() - Method in class org.intermine.api.query.range.AbstractHelper

By default the CONTAINS options are same as the WITHIN options with the left and right operators swapped.

getContent(String, boolean, String, String) - Method in class org.intermine.dwr.AjaxServices

getContent() - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig

Get the content of the widget.

getContents() - Method in class org.intermine.api.profile.InterMineBag

Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.

getContents() - Method in class org.intermine.api.profile.StorableBag

Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.

getContentsAsIds() - Method in class org.intermine.api.profile.InterMineBag

Returns a List which contains the contents of this bag as Integer IDs.

getContentsOrderByExtraValue() - Method in class org.intermine.api.profile.StorableBag

getContentType() - Method in interface org.intermine.webservice.client.core.Request

getContentType() - Method in class org.intermine.webservice.client.core.RequestImpl

getContentType() - Method in enum org.intermine.webservice.server.Format

getConversionMapQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter

Get conversion query for the types provided, edited so that the first type is constrained to be in the bag.

getConversionQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter

Get conversion query for the types provided, edited so that the first type is constrained to be in the bag and the first type is removed from the view list so that the query only returns the converted type.

getConversionTemplates() - Method in class org.intermine.api.bag.BagQueryRunner

Fetch conversion template queries from the template manager.

getConversionTemplates(List<ApiTemplate>, Class) - Static method in class org.intermine.api.bag.TypeConverter

Return a Map from typeB to a TemplateQuery that will convert from typeA to typeB.

getConversionTemplates() - Method in class org.intermine.api.template.TemplateManager

Return template queries used for converting between types in bag upload and lookup queries, these are Superuser templates that have been tagged with TagNames.IM_CONVERTER.

getConvertCountForBag(String, String) - Static method in class org.intermine.dwr.AjaxServices

For a given bag name and a type different from the bag type, give the number of converted objects

getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.web.logic.bag.BagConverter

getConvertedObjectMap(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object, ObjectStore) - Static method in class org.intermine.api.bag.TypeConverter

Converts a List of objects from one type to another type using a TemplateQuery, returns a map from an original object to the converted object(s).

getConvertedObjects(HttpSession, List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, InterMineBag) - Static method in class org.intermine.web.logic.bag.BagConversionHelper

Converts a List of objects from one type to another type using a TemplateQuery, returns the converted objects.

getConvertedValue(Class<?>) - Method in class org.intermine.objectstore.query.UnknownTypeValue

Returns the value, converted (if possible) into the object type given by the input class.

getCorrection() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions

getCorrection() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

getCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getCount() - Method in class org.intermine.api.profile.TagHandler

Return a count of the number of tags read.

getCount() - Method in class org.intermine.api.tracker.track.ListTrack

Return the number of items contained into the list

getCount() - Method in class org.intermine.web.logic.results.ReportInList

getCount() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor

Return the count set with setCount().

getCount(PathQuery) - Method in class org.intermine.webservice.client.services.QueryService

getCount(String) - Method in class org.intermine.webservice.client.services.QueryService

Returns the number of results the specified query will return.

getCount(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Returns the number of results the specified template will return.

getCount(TemplateQuery) - Method in class org.intermine.webservice.client.services.TemplateService

getCountItemsWithLengthNotNull() - Method in class org.intermine.api.profile.InterMineBag

Return the number of items contained in the bag with length not null If the type bag is not a subclass of SequenceFeature, return 0

getCounts(Profile, InterMineBag) - Method in class org.intermine.web.logic.bag.BagConverter

Method to return list of values and the counts of converted objects for that object used for display on list analysis page.

getCounts() - Method in class org.intermine.web.logic.widget.EnrichmentResults

Get the count of each attribute value found in the sample.

getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite

getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getCreatedAt() - Method in class org.intermine.webservice.client.lists.ItemList

Get the date when this list was created.

getCrossReferences() - Method in class org.intermine.bio.dataconversion.UniprotConfig

getCurrentBags(Profile) - Method in class org.intermine.api.bag.BagManager

Get the bags this user has access to, as long as they are current.

getCurrentBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager

Fetch the current user or global or shared bags that contain the given id.

getCurrentBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch global and user bags current of the specified type or a subclass of the specified type.

getCurrentFile() - Method in class org.intermine.dataconversion.FileConverter

Return the File that is currently being converted.

getCurrentPage() - Method in class org.intermine.web.tags.table.NavigationBarTag

getCurrentSavedBags() - Method in class org.intermine.api.profile.Profile

Get the value of savedBags current

getCurrentSelectedIdStrings() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return selected object ids of the current page as a String[], needed for jsp multibox.

getCurrentSelectedIdStringsList() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return selected object ids of the current page as a List.

getCurrentUserBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch user bags current of the specified type or a subclass of the specified type.

getCustomConverterCounts(String, String) - Static method in class org.intermine.dwr.AjaxServices

For a list and a converter, return types and related counts

getCvName() - Method in class org.intermine.bio.chado.ChadoCV

Return the cvName that was passed to the constructor.

getCVTermRelationshipResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory

Return the rows from the cvterm_relationship table that relate cvterms from the cv with the given name.

getCVTermResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory

Return the rows from the cvterm table that are from the cv with the given name.

getDAG(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed to construct the DAG of the data/protocols.

getData() - Method in class org.intermine.webservice.client.results.RowResultSet

getData() - Method in class org.intermine.webservice.client.results.TabTableResult

Get the raw data from this result set.

getData() - Method in class org.intermine.webservice.client.results.XMLTableResult

getDatabase() - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Return the database to read from

getDatabase() - Method in class org.intermine.dataconversion.DBConverter

Get the Database that was passed to the constructor.

getDatabase() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns the Database used by this ObjectStore

getDatabase(String) - Static method in class org.intermine.sql.DatabaseFactory

Returns a connection to the named database

getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

Return a DataSet item with the given details.

getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Return a DataSet ref with the given details.

getDataSet() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Return the DataSet to add to each object.

getDataSet() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return the DataSet Item created for this GFF3Converter from the data set title passed to the constructor.

getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return the DataSet Item created from the dataSetTitle.

getDataSetItem(String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return a DataSource item for the given name

getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return a DataSource item with the given details.

getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter

Return the DataSet Item created from the dataSetTitle.

getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return a DataSource item with the given details.

getDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return a ReferenceList containing the DataSet Items ids set by addDataSet()

getDatasetRefId() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return the DataSet title for a given taxon id.

getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Default implementation that makes a data set title based on the data source name.

getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter

Default implementation that makes a data set title based on the data source name.

getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

Return a DataSource item for the given title

getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Return a DataSource item for the given title

getDataSource() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return the DataSource Item created for this GFF3Converter from the data source name passed to the constructor.

getDataSource() - Method in class org.intermine.sql.Database

Gets the DataSource object for this Database

getDataSourceItem() - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return the DataSource Item created from the dataSourceName.

getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return a DataSet item for the given title

getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return a DataSet item for the given title

getDataSourceName() - Method in class org.intermine.bio.dataconversion.BioDBConverter

Return the data source name set by setDataSourceName().

getDataTracker() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Returns the data tracker being used.

getDateCreated() - Method in class org.intermine.api.profile.InterMineBag

Return the creation date that was passed to the constructor.

getDateCreated() - Method in class org.intermine.api.profile.InvalidBag

getDateCreated() - Method in class org.intermine.api.profile.SavedQuery

Get the date on which the query was created.

getDateCreated() - Method in class org.intermine.api.profile.StorableBag

Get the date that this bag was created at.

getDayToken() - Method in class org.intermine.api.profile.Profile

Get a token with at least an hour of validity, and up to 24 hours.

getDayToken() - Method in class org.intermine.api.util.AnonProfile

getDb() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getDbDescription() - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.

getDbDescription() - Method in class org.intermine.objectstore.query.ClobAccess

Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.

getDbDescription() - Method in class org.intermine.objectstore.query.PendingClob

Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.

getDbref() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getDbrefs() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getDbxrefResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the dbxref table.

getDbxrefs() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Dbxref field from the attributes of this record.

getDefaultClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the QueryClass that represents the collection in this object.

getDefaultClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the QueryClass that represents the collection in this object.

getDefaultEventIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getDefaultEventIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getDefaultFileName() - Method in class org.intermine.webservice.server.query.CodeService

getDefaultFileName() - Method in class org.intermine.webservice.server.query.QueryRetrieverService

getDefaultFileName() - Method in class org.intermine.webservice.server.SchemaListService

getDefaultFileName() - Method in class org.intermine.webservice.server.SummaryService

getDefaultFileName() - Method in class org.intermine.webservice.server.WebService

getDefaultFilterValue(WidgetConfig, InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService

Get the default filter value for a widget.

getDefaultFormat() - Method in class org.intermine.webservice.server.core.JSONService

getDefaultFormat() - Method in class org.intermine.webservice.server.lists.AvailableListsService

getDefaultFormat() - Method in class org.intermine.webservice.server.lists.ListMakerService

getDefaultFormat() - Method in class org.intermine.webservice.server.model.ModelService

getDefaultFormat() - Method in class org.intermine.webservice.server.path.PossibleValuesService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.CodeService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryRetrieverService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryToListService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryUploadService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.QueryResultService

getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.TableRowService

getDefaultFormat() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService

getDefaultFormat() - Method in class org.intermine.webservice.server.user.DeregistrationService

getDefaultFormat() - Method in class org.intermine.webservice.server.VersionService

getDefaultFormat() - Method in class org.intermine.webservice.server.WebService

getDefaultOperator(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the default operator to apply to new constraints.

getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.webservice.server.WebService

Make the default output for this service.

getDefaultOutput(PrintWriter, OutputStream) - Method in class org.intermine.webservice.server.WebService

Make the default output for this service.

getDefaultPermission(Profile) - Static method in class org.intermine.api.profile.ProfileManager

Wrap a profile in the default permission level.

getDefaultPropertyIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getDefaultPropertyIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Returns default style class.

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag

Returns default style class.

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag

Returns default style class.

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag

Returns default style class.

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Returns default style class.

getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag

Returns default style class.

getDefaultValue() - Method in class org.intermine.api.mines.LocalMine

getDefaultValue() - Method in interface org.intermine.api.mines.Mine

get first default value. used in querybuilder to select default extra value

getDefaultValue() - Method in class org.intermine.api.mines.RemoteMine

getDefaultValues() - Method in class org.intermine.api.mines.LocalMine

getDefaultValues() - Method in interface org.intermine.api.mines.Mine

getDefaultValues() - Method in class org.intermine.api.mines.RemoteMine

getDefaultViewForClass(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Return a list of string paths that are defined as WebConfig to be shown in results.

getDefaultViewForClass(String, Model, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Return a list of string paths that are defined as WebConfig to be shown in results.

getDeleted(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return deleted subs in the chado db.

getDeletedClasses() - Method in class org.intermine.api.profile.ModelUpdate

Return a set containing all the deleted classes

getDeletionLocationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing location for deletions (chromosome_structure_variation) objects.

getDescr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

getDescription() - Method in class org.intermine.api.mines.LocalMine

getDescription() - Method in interface org.intermine.api.mines.Mine

getDescription() - Method in class org.intermine.api.mines.RemoteMine

getDescription() - Method in class org.intermine.api.profile.InterMineBag

Return the description of this bag.

getDescription() - Method in class org.intermine.api.profile.InvalidBag

getDescription() - Method in class org.intermine.api.profile.StorableBag

getDescription() - Method in interface org.intermine.api.search.WebSearchable

Return the description of this object.

getDescription() - Method in class org.intermine.bio.ontology.OboTerm

Get the term description.

getDescription(String) - Method in class org.intermine.pathquery.PathQuery

Returns the description for a given path, or null if no description is registered.

getDescription() - Method in class org.intermine.pathquery.PathQuery

Gets the description for this PathQuery.

getDescription() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the label associated with a constraint if editing a template query constraint.

getDescription() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Get the description for a constraint.

getDescription() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getDescription() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

Get the description

getDescription() - Method in class org.intermine.web.struts.TemplateSettingsForm

Return the description.

getDescription() - Method in class org.intermine.webservice.client.lists.ItemList

getDescription() - Method in class org.intermine.webservice.client.widget.Widget

getDescription() - Method in class org.intermine.webservice.server.lists.ListInput

getDescription(int) - Static method in class org.intermine.webservice.server.StatusDictionary

getDescriptions() - Method in class org.intermine.pathquery.PathQuery

Returns an unmodifiable Map which is a copy of the current set of path descriptions of this query at the time of execution of this method.

getDescriptiveString() - Method in class org.intermine.pathquery.PathConstraintLoop

Returns a descriptive string for this constraint, mainly useful for checking uniqueness.

getDescriptor() - Method in class org.intermine.web.logic.results.DisplayCollection

Get ReferenceDescriptor for this reference.

getDescriptor() - Method in class org.intermine.web.logic.results.DisplayReference

Get ReferenceDescriptor for this reference.

getDescriptor() - Method in class org.intermine.web.logic.results.InlineList

getDescriptors(Model) - Static method in class org.intermine.dataloader.DataLoaderHelper

Build a map from class and field names to a priority-ordered List of source name Strings.

getDirectChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm

Get the direct children of this term.

getDirectDataLoader() - Method in class org.intermine.task.DirectDataLoaderTask

Return the DirectDataLoader for this Task.

getDirection() - Method in class org.intermine.pathquery.OrderElement

Returns the order direction of this OrderElement.

getDirectParents() - Method in class org.intermine.bio.chado.ChadoCVTerm

Get the direct parents of this term.

getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets the disableResultsCache configuration option.

getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Gets the disableResultsCache configuration option.

getDisplayer() - Method in class org.intermine.web.logic.config.FieldConfig

Get the displayer for that field

getDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer

Gimme my name

getDisplayerPage() - Method in class org.intermine.web.logic.results.ReportObjectField

Return path to a custom displayer

getDisplayFields() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getDisplayName() - Method in class org.intermine.web.logic.config.FieldConfig

Get the label to display in the webapp for this field.

getDisplayName() - Method in class org.intermine.web.logic.config.Type

getDisplayName() - Method in class org.intermine.web.logic.results.ReportObjectField

Get the label to display in the webapp for this field.

getDisplaySummary(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper

Create summary information of the paths currently in a query and their constraints for display in the QueryBuilder summary section.

getDocument() - Method in class org.intermine.api.lucene.KeywordSearchHit

document

getDoesntContainOptions() - Method in class org.intermine.api.query.range.AbstractHelper

By default the DOES NOT CONTAINS options are negation of the CONTAINS options.

getDoesntOverlapOptions() - Method in class org.intermine.api.query.range.AbstractHelper

By default the DOES NOT OVERLAP options are negation of the OVERLAPS options.

getDoGzip() - Method in class org.intermine.web.struts.TableExportForm

Get whether the output should be GZIPped.

getDomain() - Method in class org.intermine.api.beans.PartnerLink

getDomain() - Method in class org.intermine.api.mines.ObjectRequest

getDomainLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Get the domainLabel

getDoneAlready() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Returns the doneAlready Set, for logging purposes

getDoNotTruncate() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the doNotTruncate flag.

getDoNotTruncate() - Method in class org.intermine.web.logic.results.ReportObjectField

getDouble(String) - Method in class org.intermine.webservice.client.results.Item

Get a property known to be a double.

getDriver() - Method in class org.intermine.sql.Database

Gets the driver this Database

getECNumbers() - Method in class org.intermine.bio.dataconversion.UniprotEntry

geteditable() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getEditableConstraints(String) - Method in class org.intermine.template.TemplateQuery

For a path with editable constraints, get all the editable constraints as a List, or the empty list if there are no editable constraints on that path.

getEditableConstraints() - Method in class org.intermine.template.TemplateQuery

Returns the list of all editable constraints.

getEditablePaths() - Method in class org.intermine.template.TemplateQuery

Get the paths of all editable constraints in this template.

getEditingConstraintCode() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the constraint that is being edited or null if creating a new constraint.

getEditingView(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the view list that the user is currently editing.

getEFactors(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for the experimental factors.

getEffectiveOrderBy() - Method in class org.intermine.objectstore.query.Query

Gets the effective ORDER BY clause of this Query, such as may be used to create SQL.

getEffectiveView() - Method in class org.intermine.webservice.server.core.TableRowIterator

getElementClassDescriptors() - Method in class org.intermine.pathquery.Path

Return a List of the ClassDescriptor objects for each element of the path.

getElementId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

Return the table identifier if isTable==true.

getElements() - Method in class org.intermine.pathquery.Path

Return a list of field names, one per path element (except for the first, which is a class).

getElementsContainingField(String, String) - Method in class org.intermine.pathquery.Path

Return the indexes of elements containing the field given in input

getElementType(String) - Method in interface org.intermine.model.InterMineObject

Returns the element type of a collection by name.

getElementType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference

Returns the element type of a collection by name.

getEmail() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

getEmail() - Method in class org.intermine.webservice.server.JWTVerifier.Verification

getEmailAddress() - Method in class org.intermine.api.profile.Profile

Get this user's preferred email address.

getEmailer(Properties) - Static method in class org.intermine.web.context.EmailerFactory

getEncodedUrl() - Method in interface org.intermine.webservice.client.core.Request

getEncodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl

getEnd() - Method in interface org.intermine.api.query.range.Range

getEnd() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the end field of this record.

getEnd() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Get start value

getEnd() - Method in class org.intermine.objectstore.query.OverlapRange

Returns the right parameter.

getEnd() - Method in class org.intermine.webservice.server.core.Page

getEndClassDescriptor() - Method in class org.intermine.pathquery.Path

If the last element in the path is a reference or collection return the ClassDescriptor that the reference or collection references.

getEndClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint

getEndFieldDescriptor() - Method in class org.intermine.pathquery.Path

Return the FieldDescriptor of the last element in the path or null if the path has just one element.

getEndRow() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the index of the last row of this page

getEndType() - Method in class org.intermine.pathquery.Path

Return the type of the last element in the path, regardless of whether it is an attribute or a class.

getEnrich() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

The enrich property is the path to the value that should be enriched.

getEnrichIdentifier() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getEnrichmentWidgets() - Method in class org.intermine.webservice.client.services.WidgetService

getEnsemblIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Ensembl gene id resolver

getEnsemblIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Ensembl gene resolver

getEnsemblPrefix() - Method in class org.intermine.bio.util.OrganismData

getEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Get the equivalent object fetcher.

getEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Returns a Set of objects from the idMap or database that are equivalent to the given object, according to the primary keys defined by the given Source.

getEquivalentsFor(List<ResultsRow<Object>>) - Method in class org.intermine.dataloader.BatchingFetcher

Fetches the equivalent object information for a whole batch of objects.

getEquivalentsForObjects(List<FastPathObject>) - Method in class org.intermine.dataloader.BatchingFetcher

Fetches the equivalent object information for a whole batch of objects.

getError() - Method in interface org.intermine.api.idresolution.Job

getError() - Method in class org.intermine.api.idresolution.ResolutionJob

getError() - Method in class org.intermine.api.idresolution.UpgradeJob

getError() - Method in class org.intermine.webservice.server.output.Output

Gets the error message.

getError() - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

getErrorCorrection() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

which method of errorcorrection the user chose.

getErrorCorrection() - Method in class org.intermine.web.struts.WidgetForm

getErrorElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getErrorElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Gets the blocking error codes from the servlet context.

getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidator

Returns errors occurred during parsing xml.

getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

Returns errors occurred during parsing xml.

getErrorsAndWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator

Returns errors and warning occurred during parsing xml.

getEscapeXml() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the escapeXml flag.

getEscapeXml() - Method in class org.intermine.web.logic.results.ReportObjectField

getEstimatedRows() - Method in class org.intermine.sql.query.ExplainResult

Returns the best current estimate for the number of rows for this query.

getEstimatedSize() - Method in class org.intermine.api.results.WebResults

Get the estimated number of rows of this table

getEstimatedSize() - Method in interface org.intermine.api.results.WebTable

Get the estimated number of rows of this table

getEstimatedSize() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the (possibly estimated) number of resultElementRows of this table

getEvaluables() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint

Returns the evaluables that this object was constructed with.

getEvent() - Method in class org.intermine.api.tracker.track.ListTrack

Return the type of event to track (creation or list execution )

getEventSetDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getEventSetDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getExactSize() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the exact number of resultElementRows of this table

getException() - Method in class org.intermine.api.lucene.InterMineObjectFetcher

Get the error that occurred during processing, if any.

getExcludeList() - Method in class org.intermine.task.ConverterTask

Return the list set by setExcludeList().

getExistingBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Gets the value of existingBagName

getExistingBagName() - Method in class org.intermine.web.struts.SaveBagForm

Gets the value of existingBagName

getExistingLoops() - Method in class org.intermine.pathquery.PathQuery

Returns the set of loop constraint descriptive strings, for the purpose of checking for uniqueness.

getExperimentProperties(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for submission from the experiment_prop table.

getExperimentTitles(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for experiment from the experiment_prop table.

getExpiry() - Method in class org.intermine.webservice.server.user.DeletionToken

getExplain() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Returns the ExplainResult of this Candidate, fetching the data if not already present.

getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Internal method that creates an ExplainResult.

getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Internal method that creates an ExplainResult.

getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose

Internal method that creates an ExplainResult.

getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose

Internal method that creates an ExplainResult.

getExplainText() - Method in class org.intermine.sql.query.PostgresExplainResult

Returns the text of the explain result, in human readable form.

getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter

Do the export.

getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter

Do the export.

getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.TabHttpExporter

Do the export.

getExporter(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory

Return the exporter class for the given id.

getExportField() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getExportQuery(List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.EnrichmentWidget

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.GraphWidget

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.HTMLWidget

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidget

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidgetLdr

getExportResults(String[]) - Method in class org.intermine.web.logic.widget.Widget

getExporttype() - Method in class org.intermine.web.struts.WidgetForm

getExtension() - Method in class org.intermine.webservice.server.query.CodeService

getExtension() - Method in class org.intermine.webservice.server.WebService

getExternalLink() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getExternalLink() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getExternalLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

getExternalLinkLabel() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getExtra() - Method in class org.intermine.api.profile.BagValue

getExtraAttribute() - Method in class org.intermine.web.logic.widget.PopulationInfo

getExtraAttribute() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig

getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

Do-nothing implementation of superclass method

getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getExtraAttributes(ObjectStore, InterMineBag) - Method in interface org.intermine.web.logic.widget.WidgetHelper

Get the extra attributes needed for the DataSetLoader

getExtraConnectFieldPath() - Method in class org.intermine.web.logic.query.DisplayConstraint

getExtraConstraintClassName() - Method in class org.intermine.api.bag.BagQueryConfig

Return the class name that was passed to the constructor.

getExtraConstraintClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint

If a LOOKUP constraint and an extra value constraint is available return the classname of the extra constraint so it can be displayed.

getExtraConstraintValues() - Method in class org.intermine.web.logic.query.DisplayConstraint

If a LOOKUP constraint and an extra constraint is available for this path, return a list of the possible values for populating a dropdown.

getExtraCorrectionCoefficient() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions

getExtraCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

getExtraCorrectionCoefficient() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return an extra constraint to be used when querying the feature table.

getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Return an extra constraint to be used when querying the feature table.

getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return an extra constraint to be used when querying the feature table.

getExtraFieldValue() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Set the extra field value - the optional constraint on the bag upload page

getExtraFieldValue() - Method in class org.intermine.web.struts.BuildBagForm

Get the value to use when creating an extra constraint on a BagQuery, configured in BagQueryConfig.

getExtraFieldValue() - Method in class org.intermine.web.struts.ModifyBagDetailsForm

getExtraParams() - Method in class org.intermine.web.struts.TableExportForm

Extra parameters map for use by sub classes.

getExtraValue() - Method in interface org.intermine.api.idresolution.JobInput

getExtraValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint

A static method for getting the extra-value if there is one, or null if there is none to be got.

getExtraValue() - Method in class org.intermine.pathquery.PathConstraintLookup

Returns the extra value for this constraint.

getExtraValue() - Method in class org.intermine.template.TemplateValue

getExtraValue() - Method in class org.intermine.web.logic.bag.WebJobInput

getExtraValue() - Method in class org.intermine.web.logic.template.ConstraintInput

Returns extra value.

getExtraValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of extraValue

getExtraValue() - Method in class org.intermine.webservice.client.template.TemplateParameter

getExtraValue() - Method in class org.intermine.webservice.server.lists.ListInput

getExtraValue() - Method in class org.intermine.webservice.server.lists.ListsServiceInput

getExtraValueFieldClass() - Method in class org.intermine.web.logic.query.DisplayConstraint

getExtraValues() - Method in class org.intermine.web.struts.TemplateForm

Get the extra values

getExtraValues(String) - Method in class org.intermine.web.struts.TemplateForm

Get an extra value

getFacets() - Static method in class org.intermine.api.lucene.KeywordSearch

get list of facet fields and names

getFacets() - Method in class org.intermine.api.lucene.ResultsWithFacets

getFactory() - Static method in class org.intermine.bio.util.ClobAccessReverseComplement

Returns a ClobAccessSubclassFactory object that will access the constructor of this class quickly, in order to avoid using reflection for every clob.

getFactory() - Method in class org.intermine.webservice.client.core.Service

Get the ServiceFactory this service was constructed with.

getFastList(String, String, int) - Method in class org.intermine.web.autocompletion.AutoCompleter

Returns n search results

getFeature() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the feature Item set by setFeature()

getFeature() - Method in class org.intermine.bio.dataconversion.UniprotEntry

used to get the feature to store.

getFeatureCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the feature_cvterm/cvterm table.

getFeatureIdQuery() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return an SQL query that finds the feature_ids of all rows from the feature table that we need to process.

getFeatureLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the featureloc table.

getFeatureMap() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Fetch the populated map of chado feature id to FeatureData objects.

getFeaturePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the featureprop table.

getFeatureRelationshipResultSet(Connection, boolean) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the feature_relationship table.

getFeatures() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.

getFeatures() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.

getFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Get a list of the chado/so types of the SequenceFeatures we wish to load.

getFeatures() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getFeatures() - Method in class org.intermine.bio.dataconversion.WormBaseProcessor

Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.

getFeatureTableResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the features table.

getFeatureTypes() - Method in class org.intermine.bio.dataconversion.UniprotConfig

if NULL, all feature types will be loaded.

getField() - Method in class org.intermine.api.lucene.KeywordSearchFacet

internal field name

getField() - Method in class org.intermine.api.lucene.KeywordSearchFacetData

get single/first field or null

getField() - Method in interface org.intermine.api.results.ResultCell

getField() - Method in class org.intermine.api.results.ResultElement

Get the field value

getField() - Method in class org.intermine.webservice.server.core.TableCell

getFieldConfig(WebConfig, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper

Get a field config object for a particular descriptor.

getFieldConfig(WebConfig, ClassDescriptor, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper

Get a field config object for a particular descriptor.

getFieldConfig(String) - Method in class org.intermine.web.logic.config.Type

Return a FieldConfig for a particular field if it has been specified, otherwise return null

getFieldConfig(String, String) - Method in class org.intermine.web.logic.config.WebConfig

Return the FieldConfig for a particular field of the specified field, or null if field not configured.

getFieldConfig() - Method in class org.intermine.web.logic.results.InlineTableResultElement

getFieldConfigMap() - Method in class org.intermine.web.logic.config.Type

Return a Map from FieldConfig.fieldName to FieldConfig objects.

getFieldConfigs() - Method in class org.intermine.web.logic.config.Type

Get the List of FieldConfig objects

getFieldConfigs(String) - Method in class org.intermine.web.logic.config.WebConfig

Return a FieldConfigs for a particular class or an empty list if no config is defined.

getFieldConfigs() - Method in class org.intermine.web.logic.results.ReportObject

Return a list of field configs

getFieldConfigs() - Method in class org.intermine.web.search.KeywordSearchResult

fieldConfigs

getFieldDescriptor() - Method in class org.intermine.pathquery.Node

getFieldDescriptor() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Return the last field descriptor (the last element) of the path.

getFieldDescriptor() - Method in class org.intermine.web.logic.results.InlineResultsTable

Get the fields descriptor this list represents.

getFieldDisplayName(String) - Method in class org.intermine.web.logic.results.ReportObject

Return a string to display as the name of a field.

getFieldExporter() - Method in class org.intermine.web.logic.config.FieldConfig

Return the class name of the FieldExporter to use when this field is viewed.

getFieldExpr() - Method in class org.intermine.web.logic.config.FieldConfig

Return the JSTL expression for the object.

getFieldName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction

Return the fieldName that was passed to the constructor.

getFieldName() - Method in class org.intermine.bio.chado.config.SetFieldConfigAction

Return the field name that was passed to the constructor.

getFieldName() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the name of the field.

getFieldName() - Method in class org.intermine.objectstore.query.QueryField

Returns the name of the field.

getFieldName() - Method in class org.intermine.objectstore.query.QueryForeignKey

Gets the fieldname of this QueryReference.

getFieldName() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the name of the field.

getFieldName() - Method in class org.intermine.objectstore.query.QueryReference

Gets the fieldname of this QueryReference.

getFieldName() - Method in class org.intermine.pathquery.Node

Gets the value of fieldName

getFieldName(int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

return the fieldName at position index

getFieldName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns the fieldname for this path.

getFieldNames() - Method in class org.intermine.api.lucene.InterMineObjectFetcher

get list of fields contained in the fetched documents

getFieldNames() - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getFieldNames

getFieldNumber() - Method in class org.intermine.objectstore.query.PathExpressionField

Returns the field number.

getFieldProxy(String) - Method in class org.intermine.objectstore.proxy.ProxyReference

getFields() - Method in class org.intermine.api.lucene.KeywordSearchFacetData

array of field names, only used for path right now

getFieldToAlias(FromElement) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getFieldType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference

getFieldValue(String) - Method in class org.intermine.objectstore.proxy.ProxyReference

getFieldValue(String) - Method in class org.intermine.web.logic.results.ReportObject

Get field value for a field name (expression)

getFieldValues(String, String) - Method in class org.intermine.objectstore.ObjectStoreSummary

Get a list of the possible values (as Strings) for a given field in a given class.

getFieldValues() - Method in class org.intermine.web.search.KeywordSearchResult

values of all fields

getFieldValues(ObjectStore, ObjectStoreSummary, String, String) - Static method in class org.intermine.web.struts.BagBuildController

Return a list of the possible field values for the given class/field name combination.

getFileName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

Returns the filename that should be associated with this query.

getFilename(String, String) - Static method in class org.intermine.modelproduction.MetadataManager

Given a key and model name, return filename for reading/writing.

getFilter() - Method in interface org.intermine.web.logic.widget.WidgetOptions

getFilter() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

filter values get used in the query to constrain the results in some way, and they can be changed by the user.

getFilter() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

getFilterLabel() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getFilterLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

the label for the filter.

getFilters() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getFilters() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

filter values get used in the query to constrain the results in some way, and they can be changed by the user.

getFilters() - Method in class org.intermine.webservice.client.widget.Widget

getFiltersValues(ObjectStore, InterMineBag) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getFilterWebSearchables(HttpServletRequest, String, String, String) - Static method in class org.intermine.web.struts.WebSearchableListController

Get all the WebSearchables in the given scope and of the given type.

getFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return items that need extra processing that can only be done after all other GFF features have been read.

getFirstAlias() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Alias field from the attributes of this record.

getFirstColumnForClass(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper

Find the first column index for the specified class or a subclass in the page table (may be a parent class of a field being displayed).

getFirstOrderByHasNoNulls() - Method in class org.intermine.sql.precompute.PrecomputedTable

Returns true if the first element of the ORDER BY clause is a column that contains no nulls.

getFirstSelectedFields(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the fields for the first selected objects.

getFishIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fish id resolver

getFishIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fish id resolver

getFishIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fish id resolver

getFixedOps() - Method in class org.intermine.web.logic.query.DisplayConstraint

If a dropdown is available for a constraint fewer operations are possible, return the list of operations.

getFlatSelect() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

Converts a SELECT list from a normal query into a representation of the columns returned in this converted list.

getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidget

Get the flattened results

getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

get the flattened results

getFloat(String) - Method in class org.intermine.webservice.client.results.Item

Get a property known to be an float.

getFlyBaseMiscCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Get ChadoCV object representing the FlyBase misc cv.

getFlyBaseSequenceOntologyCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Get ChadoCV object representing SO from FlyBase.

getFlyIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fly id resolver

getFlyIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fly id resolver

getFlyIdResolver(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fly id resolver

getFlyIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fly id resolver

getFlyIdResolver(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a fly id resolver

getFooter() - Static method in class org.intermine.xml.full.FullRenderer

Return the Full XML file footer

getFormat() - Method in enum org.intermine.api.mines.ContentType

getFormat() - Method in class org.intermine.web.struts.CSVExportForm

Return the format field ("csv", "tab", ...)

getFormat() - Method in class org.intermine.webservice.server.WebService

Returns required output format.

getFormatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue

Get the formatted version, with e.g. italics tags.

getFormattedClassName() - Method in class org.intermine.web.logic.config.Type

getFormattedClassName(String) - Static method in class org.intermine.web.logic.config.Type

getFormattedName() - Method in class org.intermine.web.logic.config.FieldConfig

getFormattedName(String) - Static method in class org.intermine.web.logic.config.FieldConfig

getFormattedTrack() - Method in class org.intermine.api.tracker.track.KeySearchTrack

getFormattedTrack() - Method in class org.intermine.api.tracker.track.ListTrack

Return the track formatted into an array of String to be saved in the database

getFormattedTrack() - Method in class org.intermine.api.tracker.track.LoginTrack

Return the track formatted into an array of String to be saved in the database

getFormattedTrack() - Method in class org.intermine.api.tracker.track.QueryTrack

getFormattedTrack() - Method in class org.intermine.api.tracker.track.TemplateTrack

Return the track formatted into an array of String to be saved in the database

getFormattedTrack() - Method in interface org.intermine.api.tracker.track.Track

Return the track formatted into an array of String to be saved in the database

getFormatter() - Static method in class org.intermine.webservice.server.core.ISO8601DateFormat

getFormFile() - Method in class org.intermine.web.struts.BuildBagForm

Get the FormFile.

getFormFile() - Method in class org.intermine.web.struts.ImportXMLForm

Get the FormFile.

getFragmentFromURI(String) - Static method in class org.intermine.util.XmlUtil

Return the fragment portion of a URI string (i.e. everything after a #).

getFriendlyDesc(Object) - Static method in class org.intermine.util.DynamicUtil

Creates a friendly description of an object - that is, the class and the ID (if it has one).

getFriendlyMineLinks(String, String, String) - Static method in class org.intermine.dwr.AjaxServices

used on REPORT page For a gene, generate links to other intermines.

getFriendlyMines() - Method in class org.intermine.api.mines.FriendlyMineManager

Return a list of Mines listed in config.

getFriendlyName() - Method in class org.intermine.pathquery.Node

Gets a friendly name for display on the web site.

getFriendlyName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns the last element of the path.

getFrom() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getFrom() - Method in class org.intermine.objectstore.query.Query

Returns all FromElements in the FROM clause

getFrom() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the additional FROM list.

getFrom() - Method in class org.intermine.sql.query.Query

Gets the Set of from tables for this query.

getFromElement() - Method in class org.intermine.objectstore.query.QueryField

Gets the FromElement of which the field is a member

getFrontcolor() - Method in class org.intermine.api.mines.LocalMine

getFrontcolor() - Method in interface org.intermine.api.mines.Mine

getFrontcolor() - Method in class org.intermine.api.mines.RemoteMine

getFullName(String) - Static method in class org.intermine.webservice.server.CodeTranslator

Returns corresponding fullName of translated operation.

getGap() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Gap field from the attributes of this record.

getGeneDesignation() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

Where to get the gene identifier from. e.g. in WormBase, it's the gene ID.

getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

A string value, e.g.

getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

getGeneIdentifierFields(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

getGeneInfoRecords() - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser

Return information read from the file, for each taxon id there is one GeneInfoRecord per row in the file.

getGeneNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getGeneratedPathDescription(String) - Method in class org.intermine.pathquery.PathQuery

Returns the path description for the given path.

getGenus() - Method in class org.intermine.bio.util.OrganismData

Get the genus of this organism.

getGlobalBag(String) - Method in class org.intermine.api.bag.BagManager

Fetch a global bag by name.

getGlobalBags() - Method in class org.intermine.api.bag.BagManager

Fetch globally available bags - superuser public bags that are available to everyone.

getGlobalBagsContainingId(Integer) - Method in class org.intermine.api.bag.BagManager

Fetch global bags that contain the given id.

getGlobalBagsWithTags(List<String>) - Method in class org.intermine.api.bag.BagManager

Fetch globally available bags - superuser public bags that are available to everyone with a particular tag assigned to them

getGlobalSearchRepositories() - Static method in class org.intermine.api.search.SearchRepository

Get the search repositories registered as global repositories.

getGlobalSearchRepository(Profile) - Static method in class org.intermine.api.search.SearchRepository

Get the search repository registered as global repositories for the user specified in input.

getGlobalSearchRepository(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the SearchRepository for global (public) objects.

getGlobalTemplate(String) - Method in class org.intermine.api.template.TemplateManager

Fetch a global template by name.

getGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager

Return a map from template name to template query containing superuser templates that are tagged as public.

getGlobalTemplates(boolean) - Method in class org.intermine.api.template.TemplateManager

Return a map from template name to template query containing superuser templates that are tagged as public.

getGOEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

getGoIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a GO id resolver

getGoIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a GO id resolver

getGOTerms() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getGraphType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Get the type of this graph, e.g.

getGroupBy() - Method in class org.intermine.objectstore.query.Query

Gets the GROUP BY clause of this Query

getGroupBy() - Method in class org.intermine.sql.query.Query

Gets the Set of fields in the GROUP BY clause of this query.

getGroupedConstraintLogic() - Method in class org.intermine.pathquery.PathQuery

Returns a List of logic Strings according to the different outer join sections of the query.

getHasAvailableBags() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if there are any available bags for the type of this path.

getHasClassKeys() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if the type of this path has class keys configured.

getHasDisplayer() - Method in class org.intermine.web.logic.results.InlineTableResultElement

getHasHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject

Used from JSP

getHasMoreThanOneType() - Method in class org.intermine.web.logic.results.InlineResultsTable

getHasNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject

Used from JSP

getHasPossibleLoops() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if this path in the query has possible loop constraints that are not already in the query.

getHasResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

getHasResults() - Method in class org.intermine.web.logic.widget.GraphWidget

getHasResults() - Method in class org.intermine.web.logic.widget.HTMLWidget

getHasResults() - Method in class org.intermine.web.logic.widget.TableWidget

getHasResults() - Method in class org.intermine.web.logic.widget.Widget

getHasSubclasses() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if the original type has subclasses in the model.

getHaving() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getHaving() - Method in class org.intermine.sql.query.Query

Gets the set of constraints forming the HAVING clause of this query.

getHavingBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getHeadAttributes() - Method in class org.intermine.api.template.ApiTemplate

getHeadAttributes() - Method in class org.intermine.pathquery.PathQuery

getHeadAttributes() - Method in class org.intermine.template.TemplateQuery

getHeader(String) - Method in interface org.intermine.webservice.client.core.Request

Returns the header value.

getHeader(String) - Method in class org.intermine.webservice.client.core.RequestImpl

Returns the header value.

getHeader() - Static method in class org.intermine.xml.full.FullRenderer

Return the Full XML file header

getHeaderAttributes() - Method in class org.intermine.webservice.server.clob.SequenceService

Why is the results key "features", pray?

getHeaderAttributes() - Method in class org.intermine.webservice.server.core.JSONService

Get the header attributes to apply to the formatter.

getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListMakerService

getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService

getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListTagService

getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListUploadService

Gets the header attributes on the output object.

getHeaderAttributes() - Method in class org.intermine.webservice.server.output.Output

getHeaderAttributes() - Method in class org.intermine.webservice.server.path.PossibleValuesService

getHeaderAttributes() - Method in class org.intermine.webservice.server.search.QuickSearch

getHeaderAttributes() - Method in class org.intermine.webservice.server.user.NewUserService

getHeaderAttributes() - Method in class org.intermine.webservice.server.VersionService

getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService

getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.WidgetService

getHeaderConfigLink() - Method in class org.intermine.web.logic.config.Type

getHeaderConfigTitle() - Method in class org.intermine.web.logic.config.Type

getHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject

getHeaderLink() - Method in class org.intermine.web.logic.results.ReportObject

getHeaders() - Method in interface org.intermine.webservice.client.core.Request

Returns request headers.

getHeaders() - Method in class org.intermine.webservice.client.core.RequestImpl

Returns request headers.

getHeadResources(String, Map<String, String>) - Static method in class org.intermine.web.logic.WebUtil

Returns the resources for a particular section of the head element.

getHelper(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig

getHelpMessage() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return a help message to display alongside the constraint, this will examine the constraint type and generate and appropriate message, e.g. list the key fields for LOOKUP constraints and explain the use of wildcards.

getHelpMessage(DisplayConstraint) - Static method in class org.intermine.web.logic.query.DisplayConstraintHelpMessages

Generate a context sensitive help message for a constraint.

getHelpPage(HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil

Look at the current webapp page and subtab and return the help page and tab.

getHgncIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a HGNC human gene id resolver

getHgncIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a HGNC human gene resolver

getHide() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the hide flag.

getHighlight() - Method in class org.intermine.web.struts.WidgetForm

getHighlightedLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Returns html formatted link in which are highlighted parameters that are to be replaced. * @see #getLink(String, TemplateQuery)

getHintCount(String) - Method in class org.intermine.web.logic.results.WebState

Get the number of times a particular hint has been shown.

getHintForPage(String, WebState) - Method in class org.intermine.web.logic.help.HintManager

Fetch a hint for the given page or return null if there are no hints or all hints have been displayed the maximum number of times.

getHistory() - Method in class org.intermine.api.profile.Profile

Get the session query history.

getHits() - Method in class org.intermine.api.lucene.ResultsWithFacets

getHtmlHeadTitle() - Method in class org.intermine.web.logic.results.ReportObject

Fetch a header string to use as the page title.

getHtmlLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Generates TemplateResultService web service link.

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.BadRequestException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.InternalErrorException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.NotImplementedException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ResourceNotFoundException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceForbiddenException

getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceUnavailableException

getHttpErrorCode() - Method in exception org.intermine.webservice.server.exceptions.ServiceException

getHumanIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Human gene id resolver

getHumanIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Human gene resolver

getIcon(int) - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getIcon(int) - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getIconImage() - Method in class org.intermine.web.logic.aspects.Aspect

Get the icon Image.

getID() - Method in class org.intermine.api.mines.LocalMine

getId() - Method in interface org.intermine.api.results.ResultCell

getId() - Method in class org.intermine.api.results.ResultElement

Get the Id.

getId() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Id field from the attributes of this record.

getId() - Method in class org.intermine.bio.ontology.OboTerm

Get the id of this term.

getId() - Method in class org.intermine.bio.ontology.OboTypeDefinition

getId() - Method in interface org.intermine.model.InterMineObject

Getter for the ID field - ensures that every object in the database has an ID.

getId() - Method in class org.intermine.objectstore.proxy.ProxyReference

Gets the ID value

getId() - Method in class org.intermine.web.logic.config.InlineListObject

getId() - Method in class org.intermine.web.logic.config.TableExportConfig

Return the id of this TableExportConfig.

getId() - Method in class org.intermine.web.logic.results.DisplayReference

Get the id of the object

getId() - Method in class org.intermine.web.logic.results.ReportObject

Get the id of this object

getId() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getId() - Method in class org.intermine.web.search.KeywordSearchResult

intermine ID

getId() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

getId() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Gets element id.

getId() - Method in class org.intermine.webservice.client.results.Item

Get the internal database id of the object.

getId() - Method in class org.intermine.webservice.server.core.TableCell

getIdentifier() - Method in class org.intermine.api.beans.ObjectDetails

getIdentifier() - Method in class org.intermine.api.mines.ObjectRequest

getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.

getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask

For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.

getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask

For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.

getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.NCBIFastaLoaderTask

For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.

getIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Used from JSP

getIdentifier() - Method in class org.intermine.xml.full.Item

Get the identifier of this item.

getIdentifierFields() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

which fields in gene object we are setting, eg. primaryIdentifier or secondaryIdentifier

getIdentifierMethod(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

getIdentifierMethod(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

getIdentifierName() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

getIdentifierSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

Where we should get the identifier will either be an Xref database, e.g.

getIdentifierValue(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

getIdentifierValue(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

getIdentity() - Method in class org.intermine.webservice.server.JWTVerifier.Verification

getIdField() - Method in class org.intermine.sql.writebatch.TableBatch

Returns the idField.

getIdMap() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Returns the IdMap used.

getIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory

getIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Return an IdResolver by taxon id, if not already built then create it.

getIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Return an IdResolver by a list of taxon id, if not already built then create it.

getIdResolver(String, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Return an IdResolver by taxon id, if not already built then create it.

getIdResolver(Set<String>, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Return an IdResolver by a list of taxon ids, if not already built then create it.

getIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Return an IdResolver, if not already built then create it.

getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Return an IdResolver, if not already built then create it.

getIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory

Create a MockIdResolver

getIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

Return an IdResolver, if not already built then create it.

getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

Return an IdResolver, if not already built then create it.

getIdResolverByOrganism(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Entrez Gene Id Resolver by given taxonId

getIdResolverByOrganism(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Entrez Gene Id Resolver by given taxonId set

getIdResolverByTaxonId(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Entrez Gene Id Resolver by given taxonId

getIdResolverByTaxonId(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a Entrez Gene Id Resolver by given taxonId set

getIdResolverForMOD() - Static method in class org.intermine.bio.dataconversion.IdResolverService

getIds() - Method in interface org.intermine.api.idresolution.JobInput

getIds() - Method in class org.intermine.objectstore.query.QueryClassBag

Returns the Set of object IDs present in the bag that correspond to the type specified.

getIds(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint

Get the ids for a constraint.

getIds() - Method in class org.intermine.pathquery.PathConstraintIds

Returns the id collection that the constraint is constraining to.

getIds() - Method in class org.intermine.web.logic.bag.WebJobInput

getIdsContained(Collection<Integer>) - Method in class org.intermine.api.profile.InterMineBag

Returns a List which contains the ids given in input and contained in this bag as Integer IDs.

getIdsToDelete() - Method in class org.intermine.sql.writebatch.TableBatch

Returns the delete set.

getIdsToInsert() - Method in class org.intermine.sql.writebatch.TableBatch

Returns the insert map.

getIdsToRemove(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the IDs to remove.

getIgnoredTaxonIds() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

used for testing

getImage() - Method in class org.intermine.web.logic.config.HeaderConfigLink

getImplementations() - Method in class org.intermine.xml.full.Item

Get the interfaces implemented by this item.

getImplementClassDescriptors(String) - Method in class org.intermine.xml.full.Item

Returns the ClassDescriptors for the given implementations.

getImplements(Object, Model) - Static method in class org.intermine.xml.full.ItemFactory

Get all interfaces that an object implements.

getIncludeHeaders() - Method in class org.intermine.web.struts.TableExportForm

Return the current value of the includeHeaders flag.

getIndelResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing pairs of chromosome_structure_variation (deletions) and transposable_element_insertion_site (insertions).

getIndentation() - Method in class org.intermine.pathquery.Node

Gets the value of indentation

getIndentation() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns the number of elements in the path, where a simple class is zero.

getIndentation() - Method in class org.intermine.web.logic.TreeNode

Get the indentation

getIndex() - Method in class org.intermine.api.results.Column

Gets the value of index

getIndexSearch() - Method in class org.intermine.web.autocompletion.LuceneSearchEngine

returns the indexSearcher so we can use IndexSearcher.doc(int) to get a doc

getIndexWriter(boolean, String) - Method in class org.intermine.web.autocompletion.LuceneIndex

returns the index writer

getIndirectAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getIndirectionTableName(CollectionDescriptor) - Static method in class org.intermine.sql.DatabaseUtil

Creates an indirection table name for a many-to-many collection descriptor

getIndirectionTableNames(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil

Given a ClassDescriptor find names of all related indirection tables.

getInfo() - Method in class org.intermine.api.results.WebResults

Return the ResultsInfo object from the underlying Results object.

getInfo() - Method in interface org.intermine.api.results.WebTable

Gets the underlying results object info

getInfo() - Method in interface org.intermine.objectstore.proxy.LazyCollection

Returns Returns the current best estimate of the characteristics of the LazyCollection

getInfo() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Returns Returns the current best estimate of the characteristics of the LazyCollection

getInfo() - Method in class org.intermine.objectstore.query.Results

Gets the best current estimate of the characteristics of the query.

getInfo() - Method in class org.intermine.objectstore.query.ResultsBatches

Gets the best current estimate of the characteristics of the query.

getInfoCache() - Method in class org.intermine.api.query.WebResultsExecutor

Returns the entire infoCache, which is an unmodifiable Map from PathQuery (by identity) to ResultsInfo.

getInitialExportPaths(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter

The initial export path list is just the paths from the columns of the PagedTable.

getInitialExportPaths(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter

Return a list of the Paths to show the user as initial export columns or header contents.

getInlineListConfig() - Method in class org.intermine.web.logic.config.Type

getInput() - Method in class org.intermine.api.idresolution.ResolutionJob

getInput() - Method in class org.intermine.webservice.server.lists.AbstractListService

getInput() - Method in interface org.intermine.webservice.server.lists.ListMaker

getInput() - Method in class org.intermine.webservice.server.lists.ListOperationService

getInput() - Method in class org.intermine.webservice.server.lists.ListsRequestParser

Returns parameters of web service as a parameter object.

getInput() - Method in class org.intermine.webservice.server.lists.ListSubtractionService

getInput() - Method in class org.intermine.webservice.server.lists.ListUploadService

Parse the parameters for this request.

getInput() - Method in class org.intermine.webservice.server.query.result.QueryResultRequestParser

Returns parsed parameters in parameter object - so this values can be easily get from this object.

getInput() - Method in class org.intermine.webservice.server.template.result.TemplateResultRequestParser

Returns parsed parameters in parameter object - so this values can be easily obtained from this object.

getInput(HttpServletRequest) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser

Returns parameters of web service as a parameter object.

getInputIdent() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult

getInputIdentifiersForIssue(String) - Method in class org.intermine.api.bag.BagQueryResult

getInsertionLocationsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing pairs of insertion feature_ids (eg. for "FBti0027974" => "FBti0023081") and the fmin and fmax of the first insertion in the pair (ie. the progenitor).

getInstance(ProfileManager) - Static method in class org.intermine.api.bag.SharedBagManager

Return the singleton SharedBagManager instance

getInstance() - Static method in class org.intermine.api.idresolution.IDResolver

getInstance(InterMineAPI, Properties) - Static method in class org.intermine.api.mines.FriendlyMineManager

Get an instance of FriendlyMineManager.

getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.KeySearchTracker

Return an instance of the KeySearchTracker

getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.ListTracker

Return an instance of the ListTracker

getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.LoginTracker

Return an instance of the LoginTracker

getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.QueryTracker

Return an instance of the QueryTracker

getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.TemplateTracker

Return an instance of the TemplateTracker

getInstance(String, Properties) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Creates a new instance of this class, given the properties defining it.

getInstance(String, Properties, Class<? extends IntegrationWriterDataTrackingImpl>, Class<? extends DataTracker>) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Creates a new IntegrationWriter instance of the specified class and with a specified DataTracker class plus properties.

getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Gets an ObjectStoreFastCollectionsForTranslatorImpl instance for the given properties

getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Gets an ObjectStoreFastCollectionsImpl instance for the given properties

getInstance(String, Properties) - Static method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets a ObjectStoreInterMineImpl instance for the given underlying properties

getInstance(String, Properties) - Static method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Gets an ObjectStore for the given underlying properties.

getInstance() - Static method in class org.intermine.pathquery.PathLengthComparator

getInstance(Database) - Static method in class org.intermine.sql.precompute.OptimiserCache

Returns an OptimiserCache object relevant to the database given.

getInstance(Connection) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager

Gets a PrecomputedTableManager instance for the given underlying Connection.

getInstance(Database) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager

Gets a PrecomputedTableManager instance for the given underlying database.

getInstance(String, Connection) - Static method in class org.intermine.sql.query.ExplainResult

Constructs an instance of ExplainResult for a given query String and database Connection.

getInstance(Query, Connection) - Static method in class org.intermine.sql.query.ExplainResult

Constructs an instance of ExplainResult for a given Query and database Connection.

getInstance(PreparedStatement) - Static method in class org.intermine.sql.query.ExplainResult

Constructs an instance of ExplainResult given a PreparedStatement object.

getInstance() - Static method in class org.intermine.util.AlwaysSet

Returns a new AlwaysSet with the correct type parameters.

getInstance() - Static method in class org.intermine.util.IdentityMap

Obtain an instance of this class

getInstance() - Static method in class org.intermine.util.ShutdownHook

Get the instance of this ShutdownHook.

getInstance(WebConfig, InterMineAPI) - Static method in class org.intermine.web.displayer.DisplayerManager

Fetch the DisplayerManager, a single instance is held.

getInstance(Properties) - Static method in class org.intermine.web.logic.help.HintManager

Return an instance of a HintManager.

getInstance() - Static method in class org.intermine.webservice.server.user.DeletionTokens

getInt(String) - Method in class org.intermine.webservice.client.results.Item

Get a property known to be an integer.

getIntegrationWriter() - Method in class org.intermine.dataloader.DataLoader

Return the IntegrationWriter that was passed to the constructor.

getIntegrationWriter(String) - Static method in class org.intermine.dataloader.IntegrationWriterFactory

Return an IntegrationWriter configured using properties file

getIntegrationWriter() - Method in class org.intermine.task.DirectDataLoaderTask

Return the IntegrationWriter for this task.

getInteractionResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return a result set containing the interaction genes pairs, the title of the publication that reported the interaction and its pubmed id.

getInterMineAPI() - Static method in class org.intermine.web.context.InterMineContext

getInterMineAPI(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the InterMineAPI which provides access to core features of an InterMine application.

getInterMineAPI(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the InterMineAPI which provides the core features of an InterMine application.

getInterMineAPI(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the InterMineAPI which provides access to core features of an InterMine application.

getInterMineResults() - Method in class org.intermine.api.results.WebResults

Return the underlying results object.

getIntParameter(String) - Method in class org.intermine.webservice.server.WebService

Get the value of a parameter that should be interpreted as an integer.

getIntParameter(String, Integer) - Method in class org.intermine.webservice.server.WebService

Get the value of a parameter that should be interpreted as an integer.

getIntResponse(Request) - Method in class org.intermine.webservice.client.core.Service

Performs the request and returns the result as an integer.

getIntroText() - Method in class org.intermine.web.logic.aspects.Aspect

Get the introduction text.

getIntSessionProperty(HttpSession, String, int) - Static method in class org.intermine.web.logic.WebUtil

Lookup an Integer property from the SessionContext and return it.

getInvalidBags() - Method in class org.intermine.api.profile.BagSet

getInvalidBags() - Method in class org.intermine.api.profile.Profile

getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

getInvite() - Method in class org.intermine.web.struts.InvitationForm

getInviteData(ProfileManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite

getInvitee() - Method in class org.intermine.api.bag.SharingInvite

getInvitee() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getInviterId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getInvites(InterMineAPI, Profile) - Static method in class org.intermine.api.bag.SharingInvite

Get the invitations this profile has made.

getInvites(ProfileManager, BagManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite

Get the invitations this profile has made.

getInwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil

Creates a column name for the "inward" key of a many-to-many collection descriptor.

getIqlQuery() - Method in class org.intermine.objectstore.query.Query

Returns an IqlQuery object representing this query, that may have been cached.

getIsDottedPath() - Method in class org.intermine.web.logic.config.FieldConfig

getIsKeyField() - Method in class org.intermine.web.logic.results.InlineTableResultElement

getIsNull() - Method in class org.intermine.web.logic.query.MetadataNode

getIsoforms() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getIsoformSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry

if an isoform has two ID tags, then the first one is used and the second one is added as a synonym

getIsRelative() - Method in class org.intermine.web.logic.WebUtil.HeadResource

getIssueIds() - Method in class org.intermine.api.bag.BagQueryResult

Get ids of all InterMineObjects returned that were issues for this bag query lookup.

getIssueIds(String) - Method in class org.intermine.api.bag.BagQueryResult

Get ids of all InterMineObjects returned that were registered as issues of this particular type for this bag query lookup.

getIssuer() - Method in class org.intermine.webservice.server.JWTVerifier.Verification

getIssueResults(String) - Method in class org.intermine.api.bag.BagQueryResult

getIssues() - Method in class org.intermine.api.bag.BagQueryResult

Get any results that require some user input before adding to the bag.

getItem() - Method in class org.intermine.api.search.SearchResult

Get the web searchable item that was found.

getItemElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getItemElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getItemRgb() - Method in class org.intermine.bio.io.bed.BEDRecord

getItemRgb() - Method in class org.intermine.bio.io.gaf.GAFRecord

getItems() - Method in class org.intermine.api.lucene.KeywordSearchFacet

list of all values and counts

getItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return all items set and created in handler in this run - excludes sequence and ComputationalAnalysis items.

getItems() - Method in class org.intermine.dataconversion.MockItemWriter

Get the items that have been stored This method is not part of ItemWriter, and for testing convenience returns XML Items

getItems() - Method in class org.intermine.web.logic.results.InlineList

getItems() - Method in class org.intermine.web.logic.results.InlineResultsTableRow

getItems() - Method in class org.intermine.xml.full.FullHandler

Return the Items that have been read with this handler.

getItemWriter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Return an ItemWriter used to handle the resultant Items

getItemWriter() - Method in class org.intermine.dataconversion.DataConverter

Return the ItemWriter that was passed to the constructor.

getIterator() - Method in class org.intermine.webservice.client.results.JSONResult

getIterator() - Method in class org.intermine.webservice.client.results.TabTableResult

Get a memory efficient iterator over the result rows as lists

getIterator() - Method in class org.intermine.webservice.client.results.XMLTableResult

getJavaClass() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the Java class name of the controller for this displayer.

getJobById(UUID) - Method in class org.intermine.api.idresolution.IDResolver

getJobById(String) - Method in class org.intermine.api.idresolution.IDResolver

getJobs() - Method in class org.intermine.api.idresolution.IDResolver

getJoinPath() - Method in class org.intermine.webservice.server.core.SubTable

getJoinType() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

getJson() - Method in class org.intermine.pathquery.PathQuery

toJson synonym for JSPs.

getJSONResponse(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Performs the request and returns a JSONResult containing the data.

getJSONResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService

getJSONResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Fetch some results as a list of JSON Objects.

getJSONResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Returns a subset of the results for the given template template with the given parameters, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).

getJSONResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService

getJspName() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the name of the JSP associated with this displayer.

getJspPage() - Method in class org.intermine.web.displayer.ReportDisplayer

The JSP page that will be called with the request to render output.

getKey() - Method in interface org.intermine.util.ReferenceMap.ReferenceWithKey

Returns the key in the entry.

getKey() - Method in class org.intermine.web.logic.WebUtil.HeadResource

getKey() - Method in class org.intermine.webservice.server.core.Pair

getKeyFieldNames(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper

Return names of the key fields for a given class.

getKeyFieldNames() - Method in class org.intermine.api.profile.InterMineBag

Return a list containing the keyFieldNames for the bag

getKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper

Return the key fields of a given class.

getKeyFields() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the key fields for this path as a formatted string, for use in LOOKUP help message.

getKeyFields() - Method in class org.intermine.web.search.KeywordSearchResult

key field expressions

getKeyFieldValue(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper

Get a key field value for the given object.

getKeyFieldValues(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper

Get a list of key field values for the given object.

getKeyProperties(Source) - Static method in class org.intermine.dataloader.DataLoaderHelper

Return the Properties that enumerate the keys for this Source

getKeyStore() - Static method in class org.intermine.web.context.InterMineContext

getKeywords() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getKeywordSearches(Connection) - Method in class org.intermine.api.tracker.KeySearchTracker

Return the number of search for each keyword

getKeywordSearches() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the number of search for each keyword

getLabel() - Method in class org.intermine.web.logic.config.FieldConfig

The human readable label for this field.

getLabel() - Method in class org.intermine.web.logic.config.Type

Get the label property's value.

getLabel() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption

Get the value to be displayed in the dropdown for this operation.

getLabel() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

label for the results table.

getLabel() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

Get the label for this trail element.

getLabels() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.

getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentResults

Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.

getLabels(GraphWidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl

Get the labels for Graph widgets.

getLabs(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the lab name.

getLargeImage() - Method in class org.intermine.web.logic.aspects.Aspect

Webapp relative path to large image.

getLastClassDescriptor() - Method in class org.intermine.pathquery.Path

Returns the last ClassDescriptor in the path.

getLastClassName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Fetch the unqualified class name of the final class on this path, if the path represents an attribute this will be the parent class of that attribute.

getLastElement() - Method in class org.intermine.pathquery.Path

Return the last string element of this path, throw an exception of there is only one element, i.e. for 'Company.departments.manager' return 'manager'.

getLayout() - Method in class org.intermine.web.logic.template.TemplateResultInput

getLayout() - Method in class org.intermine.webservice.server.query.result.QueryResultInput

getLdr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

getLeft() - Method in class org.intermine.objectstore.query.OverlapConstraint

Returns the left OverlapRange.

getLeft() - Method in class org.intermine.sql.query.Constraint

Returns the left argument of the constraint.

getLeft() - Method in class org.intermine.sql.query.InListConstraint

Returns the left AbstractValue.

getLeft() - Method in class org.intermine.sql.writebatch.Row

Returns left.

getLeftArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Get the left argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.

getLeftColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Returns the left column name.

getLeftField() - Method in class org.intermine.api.query.range.ConstraintOptions

Defaults to "start".

getLeftOp() - Method in class org.intermine.api.query.range.ConstraintOptions

getLength() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getLength() - Method in class org.intermine.web.logic.results.InlineList

getLengthWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess

Returns the (possibly uninitialised) length internal parameter in this object, for use by subclass constructors.

getLevel() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

getLibraryCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the librarycvterm table.

getLibraryFeatureResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the libraryprop table.

getLimit() - Method in class org.intermine.objectstore.query.Query

Returns the LIMIT parameter for this query.

getLimit() - Method in class org.intermine.sql.precompute.LimitOffsetQuery

Getter for limit.

getLimit() - Method in class org.intermine.sql.query.Query

Gets the LIMIT number for this query.

getLimit() - Method in class org.intermine.webservice.server.WebServiceInput

Returns maximum number of results the user will accept.

getLineBreak() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getLineBreak() - Method in class org.intermine.webservice.server.WebService

getLineLength() - Method in class org.intermine.web.logic.config.InlineListConfig

getLineLength() - Method in class org.intermine.web.logic.results.InlineList

getLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

the link is the class that generates the url for each result.

getLink() - Method in class org.intermine.web.struts.WidgetForm

getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag

getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Returns link switching between displayed and hidden state.

getLink(String, String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator

Generates QueryResultService web service link.

getLinkPath(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator

Get the link path for a query.

getLinkPath(TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Returns the path section of the link for this template.

getLinkPath(TemplateQuery, String) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Returns the path section of the link for this template.

getLinkPath(TemplateQuery, String, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Returns the path section of the link for this template.

getLinkRedirect() - Method in class org.intermine.api.results.ResultElement

getLinkRedirect() - Method in class org.intermine.web.search.KeywordSearchResult

URL set in web.properties.

getLinkRedirector() - Method in interface org.intermine.api.API

getLinkRedirector() - Method in class org.intermine.api.InterMineAPI

getLinks(MultiKey) - Method in class org.intermine.api.mines.FriendlyMineManager

getLinks(Mine, Mine, ObjectRequest) - Method in interface org.intermine.web.displayer.InterMineLinkGenerator

Query other intermines for this object

getLinks(FriendlyMineManager, String, String, String) - Method in class org.intermine.web.util.InterMineLinkGenerator

Query other intermines for this object

getList(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter

returns a string array with the search results of the query in the field

getList(String) - Method in class org.intermine.webservice.client.services.ListService

Returns an object representing a list on the server.

getList(Profile, String) - Method in class org.intermine.webservice.server.query.QueryListAppendService

Get a list from a profile, throwing a service forbidden exception if the list is not accessible.

getListCreationTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices

getListCreationTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getListExecutionTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices

getListExecutionTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getListIterator() - Method in class org.intermine.webservice.client.results.RowResultSet

Get a memory efficient iterator over the result rows as lists

getListLeft() - Method in class org.intermine.web.struts.ModifyBagForm

getListManager() - Method in class org.intermine.webservice.server.WebService

getListMap() - Method in class org.intermine.webservice.client.services.ListService

Returns a map from list-name to list.

getListMap() - Method in class org.intermine.webservice.server.core.ListManager

Returns the lists available to the current user in a Map.

getListName() - Method in class org.intermine.webservice.server.lists.ListInput

getListOfTypes() - Method in class org.intermine.web.logic.results.InlineResultsTable

getListOperations(Connection) - Method in class org.intermine.api.tracker.ListTracker

Return the operations done for each list (execution or creation)

getListOperations() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the operations done for each list (execution or creation)

getListPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getListRight() - Method in class org.intermine.web.struts.ModifyBagForm

getLists() - Method in class org.intermine.webservice.server.core.ListManager

Returns the lists available to the current user.

getLists() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput

getLists() - Method in class org.intermine.webservice.server.lists.AvailableListsService

Get the lists for this request.

getLists() - Method in class org.intermine.webservice.server.lists.ListInput

getLists() - Method in class org.intermine.webservice.server.lists.ListsService

Executes service specific logic.

getListsButton() - Method in class org.intermine.web.struts.ModifyBagForm

getListsContaining(Integer) - Method in class org.intermine.webservice.server.core.ListManager

Returns the current lists available to the current user which contain the specified object.

getListService() - Method in class org.intermine.webservice.client.core.ServiceFactory

Return a new ListService for getting getting list information from.

getListsMatching(ListManager, String) - Method in class org.intermine.webservice.server.lists.AvailableListsService

Get the lists that match the current filter.

getListsNames(Integer) - Method in class org.intermine.webservice.server.core.ListManager

Returns public current lists that contain object with specified id.

getListsWithObject(String, String) - Method in class org.intermine.webservice.client.services.ListService

Returns all accessible InterMine lists containing the object corresponding to the specified publicId.

getListsWithObject(int) - Method in class org.intermine.webservice.client.services.ListService

Returns all accessible InterMine public lists containing the object with the specified DB identifier.

getListUploadTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser

Return a tokeniser suitable for parsing tokens received from a list upload context.

getLocalMine() - Method in class org.intermine.api.mines.FriendlyMineManager

getLocatedGenesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return from chado the feature_ids of the genes with entries in the featureloc table.

getLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the location Item set by setLocation()

getLocationFromHeader(String, SequenceFeature, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Return a Location object create by parsing the useful information from a FlyBase fasta header line.

getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns the log used by this objectstore.

getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Returns the log used by this objectstore.

getLogarithmMap(String, TemplateManager) - Method in class org.intermine.api.tracker.TemplatesExecutionMap

Return a map containing the logarithm's sum of the templates executions launched by the same users or during the same sessions.

getLogarithmMap(String, String, TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker

Return a map containing the logarithm of accesses for each template.

getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets the logBeforeExecute configuration option.

getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Gets the logBeforeExecute configuration option.

getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets the logEverything configuration option.

getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Gets the logEverything configuration option.

getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets the logExplains configuration option.

getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Gets the logExplains configuration option.

getLogicExpression() - Method in class org.intermine.pathquery.PathQuery

getLoginTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getLogo() - Method in class org.intermine.api.mines.LocalMine

getLogo() - Method in interface org.intermine.api.mines.Mine

getLogo() - Method in class org.intermine.api.mines.RemoteMine

getLongDisplayers() - Method in class org.intermine.web.logic.config.Type

Get the List of long Displayers

getLookupOp() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the LOOKUP constraint op.

getLookupOs() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Returns the objectstore that contains the equivalent objects.

getLookupTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser

Return a tokeniser suitable for parsing tokens received from a lookup constraint context.

getLoopPath() - Method in class org.intermine.pathquery.PathConstraintLoop

Returns the path that the constraint is constraining to.

getLoopQueryOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of loopQueryOp

getLoopQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the set of operators valid for loop constraints.

getLoopQueryValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of loopQueryValue

getMailinglist() - Method in class org.intermine.web.struts.CreateAccountForm

getMainIds() - Method in class org.intermine.bio.dataconversion.GeneInfoRecord

Return the entrez gene id, official symbol and default symbol (if different).

getMainSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions

getMainSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter

Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.

getMainSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.

getMainTitles() - Method in class org.intermine.web.logic.config.Type

getMap() - Method in class org.intermine.util.DynamicBean

Getter for the map, for testing purposes

getMapIterator() - Method in class org.intermine.webservice.client.results.RowResultSet

Get a memory efficient iterator over the result rows as lists

getMapper(TagMapper.Field) - Static method in class org.intermine.api.profile.TagMapper

Get a tag mapper.

getMatchAndIssueIds() - Method in class org.intermine.api.bag.BagQueryResult

Get ids of all InterMineObjects returned that were matches or issues for this bag query lookup.

getMatcher() - Method in class org.intermine.webservice.server.lists.ListUploadService

Get the String Matcher for parsing the list of identifiers.

getMatches() - Method in class org.intermine.api.bag.BagQueryResult

Get any exact matches found by the queries [id -> [input strings].

getMatchIDs() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Get the encoded match ids (hidden form field).

getMatchLocResultSet(Connection, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Return the interesting feature (EST, UST, RST, other?)

getMatchLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting matches from the featureloc and feature tables.

getMatchOnFirst() - Method in class org.intermine.api.bag.BagQueryConfig

If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.

getMatchTypesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Return the match types, used to determine which additional query to run This is a protected method so that it can be overridden for testing

getMaterialisedCollection() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Gets the collection if it is a real materialised collection.

getMax(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Return the maximum coordinate of the given location

getMax() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns the maximum possible number of rows in the results.

getMax() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

maximum value to display.

getMax() - Method in class org.intermine.web.struts.WidgetForm

getMax() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary

getMaxLimit() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException

getMaxLimit() - Method in interface org.intermine.objectstore.ObjectStore

Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException

getMaxLimit() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException

getMaxLimit() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException

getMaxOffset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException

getMaxOffset() - Method in interface org.intermine.objectstore.ObjectStore

Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException

getMaxOffset() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException

getMaxOffset() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException

getMaxParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction

getMaxPValue() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions

getMaxPValue() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

getMaxQueryParseTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

getMaxQueryParseTime() - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Get the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.

getMaxRetrievableIndex() - Method in class org.intermine.api.results.WebResults

Returns the ObjectStore's maximum allowable offset.

getMaxRetrievableIndex() - Method in interface org.intermine.api.results.WebTable

Return the maximum retrievable index for this PagedTable.

getMaxRetrievableIndex() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the maximum retrievable index for this PagedTable.

getMaxSize() - Method in class org.intermine.objectstore.query.ResultsBatches

Returns the current maximum number of rows in the results

getMaxTime() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException

getMaxTime() - Method in interface org.intermine.objectstore.ObjectStore

Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException

getMaxTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException

getMaxTime() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException

getMaxValues() - Method in class org.intermine.objectstore.ObjectStoreSummary

Return the configured maximum number of values to show in a dropdown.

getMd5checksum() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getMessage() - Method in class org.intermine.api.bag.BagQuery

Return the message that was passed to the constructor.

getMessage() - Method in class org.intermine.web.struts.ContactForm

getMessage() - Method in exception org.intermine.webservice.client.exceptions.ResultException

getMessage() - Method in exception org.intermine.webservice.client.exceptions.ServiceException

getMessage() - Method in exception org.intermine.webservice.server.exceptions.ServiceException

getMessageElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getMessageElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getMessageFormat() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getMessageFormat() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getMessageFormat() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getMethod() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig

getMethodDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getMethodDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getMimeType() - Method in enum org.intermine.api.mines.ContentType

getMin(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Return the minimum coordinate of the given location

getMin() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns the minimum possible number of rows in the results.

getMin() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary

getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns the cutoff value used to decide if a bag should be put in a table.

getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Returns the cutoff value used to decide if a bag should be put in a table.

getMine(String) - Method in class org.intermine.api.mines.FriendlyMineManager

getMineId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput

getMineResultsLink(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator

Get the link for a query that shows the results in a mine.

getMineResultsLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Get a link that takes the user to a results page in the originating mine.

getMineResultsPath(String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator

Get the link path for a query that shows the results in a mine.

getMineResultsPath(TemplateQuery, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Get a link that takes the user to a results page in the originating mine.

getMinimalPath() - Method in class org.intermine.pathquery.Node

getMinParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction

getMinSize() - Method in class org.intermine.objectstore.query.ResultsBatches

Returns the current minimum number of rows in the results

getMissingTables() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns the Set of table names which are tables missing from the database.

getMockIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a mock id resolver for unit test

getMode() - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Returns the optimiser mode of operation.

getModel() - Method in interface org.intermine.api.API

getModel() - Method in class org.intermine.api.InterMineAPI

getModel() - Method in class org.intermine.api.mines.LocalMine

getModel() - Method in interface org.intermine.api.mines.Mine

Get the main model associated with this application.

getModel() - Method in class org.intermine.api.mines.RemoteMine

getModel() - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Return the Model of the target database.

getModel() - Method in class org.intermine.bio.ontology.SequenceOntology

getModel() - Method in class org.intermine.dataconversion.DataConverter

Return the data Model that was passed to the constructor.

getModel() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Returns the Model used.

getModel() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Return the metadata associated with this ObjectStore

getModel() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns the model.

getModel() - Method in interface org.intermine.objectstore.ObjectStore

Return the metadata associated with this ObjectStore

getModel() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Return the metadata associated with this ObjectStore

getModel() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Return the metadata associated with this ObjectStore

getModel() - Method in class org.intermine.pathquery.Path

Return the model that this path is created for.

getModel() - Method in class org.intermine.pathquery.PathQuery

Returns the Model object stored in this object.

getModel() - Method in class org.intermine.webservice.client.core.ServiceFactory

A convenience method to getting a model (used widely throughout the API).

getModel() - Method in class org.intermine.webservice.client.services.ModelService

Returns the model used by the InterMine instance which the service is connected to.

getModel() - Method in class org.intermine.xml.full.Item

Return the model that was passed to the constructor or set with setModel().

getModelFromClasspath(String, Properties) - Static method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Read the Model from the classpath.

getModelName() - Method in class org.intermine.task.ConverterTask

Return the model name

getModelService() - Method in class org.intermine.webservice.client.core.ServiceFactory

Return a new ModelService for retrieving the data model.

getModelXml() - Method in class org.intermine.webservice.client.services.ModelService

An method used internally to fetch the XML for the model from the server.

getModifiableEditableConstraints() - Method in class org.intermine.template.TemplateQuery

Returns the list of all editable constraints.

getMolecularWeight() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getMonkey() - Method in class org.intermine.web.struts.ContactForm

getMostPopularTemplateOrder(Integer) - Method in class org.intermine.api.template.TemplateManager

Return the list of public templates ordered by rank descendant.

getMostPopularTemplateOrder(String, String, Integer) - Method in class org.intermine.api.template.TemplateManager

Return the template list ordered by rank descendant for the user/sessionid specified in the input

getMouseIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a mouse id resolver

getMouseIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a mouse id resolver

getMouseIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a mouse id resolver

getMrlv() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

Returns the MultiRowLaterValue corresponding to this object.

getMRNA(String, Organism, Model) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Create an MRNA with the given primaryIdentifier and organism or return null of MRNA is not in the data model.

getMultiValueAttribute() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Returs the value of multiValueAttribute

getMultiValueAttribute() - Method in class org.intermine.web.struts.TemplateForm

Returns the multivalueattribute

getMultiValueAttribute(String) - Method in class org.intermine.web.struts.TemplateForm

Returns the multivalueattribute given a key

getMultiValues() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the value collection if the constraint is a multivalue, otherwise return null.

getMultivalues() - Method in class org.intermine.web.logic.template.ConstraintInput

Return multivalues

getMultiValues() - Method in class org.intermine.web.struts.TemplateForm

Returns the multiValues

getMultiValues(String) - Method in class org.intermine.web.struts.TemplateForm

Get a multi value

getMultiValuesAsString() - Method in class org.intermine.web.logic.query.DisplayConstraint

If the constraint is a multivalue, returns the value collection represented as string separated by ', ', otherwise return an empty String.

getName() - Method in class org.intermine.api.beans.ObjectDetails

getName() - Method in class org.intermine.api.lucene.KeywordSearchFacet

user-friendly name

getName() - Method in class org.intermine.api.lucene.KeywordSearchFacetData

name of the facet (displayed on page)

getName() - Method in class org.intermine.api.mines.LocalMine

getName() - Method in interface org.intermine.api.mines.Mine

getName() - Method in class org.intermine.api.mines.RemoteMine

getName() - Method in class org.intermine.api.profile.InterMineBag

Returns the value of name

getName() - Method in class org.intermine.api.profile.InvalidBag

getName() - Method in class org.intermine.api.profile.Profile

Return a first part of the username before the "@" sign (used in metabolicMine)

getName() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

getName() - Method in class org.intermine.api.profile.SavedQuery

Get the name of the saved query.

getName() - Method in class org.intermine.api.profile.StorableBag

getName() - Method in interface org.intermine.api.profile.Taggable

The name (or identifier) used as the primary key for storing this object.

getName() - Method in exception org.intermine.api.query.BagNotFound

getName() - Method in class org.intermine.api.results.Column

Get the name (title) of the column.

getName() - Method in class org.intermine.api.tracker.AbstractTracker

Return the tracker's name

getName() - Method in class org.intermine.api.tracker.KeySearchTracker

getName() - Method in class org.intermine.api.tracker.ListTracker

Return the tracker's name

getName() - Method in class org.intermine.api.tracker.LoginTracker

Return the tracker's name

getName() - Method in class org.intermine.api.tracker.QueryTracker

Return the tracker's name

getName() - Method in class org.intermine.api.tracker.TemplateTracker

Return the tracker's name

getName() - Method in interface org.intermine.api.tracker.Tracker

Return the tracker's name

getName() - Method in class org.intermine.bio.chado.ChadoCVTerm

Return the name of this term.

getName() - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder

getName() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getName() - Method in class org.intermine.bio.io.bed.BEDRecord

getName() - Method in class org.intermine.bio.io.gaf.GAFRecord

getName() - Method in class org.intermine.bio.ontology.OboTerm

Get the name of this term.

getName() - Method in class org.intermine.bio.ontology.OboTermSynonym

Get the synonym name.

getName() - Method in class org.intermine.bio.ontology.OboTypeDefinition

getName() - Method in class org.intermine.dataloader.Source

Getter for name.

getName() - Method in class org.intermine.pathquery.LogicExpression.Variable

Get variable name.

getName() - Method in class org.intermine.sql.Database

Gets the database name only, not the full URL.

getName() - Method in class org.intermine.sql.precompute.PrecomputedTable

Gets the name of this PrecomputedTable

getName() - Method in class org.intermine.sql.query.Field

Returns the name of the field.

getName() - Method in class org.intermine.sql.query.Table

Returns the name of the table

getName() - Method in class org.intermine.template.TemplateQuery

Get the query short name.

getName() - Method in class org.intermine.web.logic.aspects.Aspect

Get the name of the data set.

getName() - Method in class org.intermine.web.logic.aspects.AspectSource

Get the source name.

getName() - Method in class org.intermine.web.logic.results.ReportObjectField

Get field name

getName() - Method in class org.intermine.web.logic.template.TemplateResultInput

Returns template name.

getName() - Method in class org.intermine.web.struts.ContactForm

getName() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getName() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getName() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

getName() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getName() - Method in class org.intermine.web.struts.TemplateForm

Get the template name.

getName() - Method in class org.intermine.web.struts.TemplateSettingsForm

getName() - Method in class org.intermine.webservice.client.lists.ItemList

Get the name of this list.

getName() - Method in class org.intermine.webservice.client.widget.Widget

getName() - Method in class org.intermine.xml.full.Attribute

Get the name of this field

getName() - Method in class org.intermine.xml.full.Reference

Get the name of this field

getName() - Method in class org.intermine.xml.full.ReferenceList

Get the name of this field.

getNames() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the list of the Name field from the attributes of this record.

getNameSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

getNamespace() - Method in class org.intermine.bio.ontology.OboTerm

Get the namespace attribute.

getNewBagName() - Method in class org.intermine.api.bag.operations.BagOperation

getNewBagName() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Get the bag name.

getNewBagName() - Method in class org.intermine.web.struts.ModifyBagForm

Get the new bag name.

getNewBagName() - Method in class org.intermine.web.struts.SaveBagForm

Gets the value of newBagName

getNewBagType() - Method in class org.intermine.api.bag.operations.BagOperation

getNewBagType() - Method in class org.intermine.api.bag.operations.Intersection

getNewBagType() - Method in class org.intermine.api.bag.operations.RelativeComplement

getNewBagType() - Method in class org.intermine.api.bag.operations.SymmetricDifference

getNewBagType() - Method in class org.intermine.api.bag.operations.Union

getNewBagType() - Method in class org.intermine.web.struts.TriageBagForm

Get the new bag name.

getNewData() - Method in class org.intermine.dataloader.ObjectDescription

Returns the new data, which needs to be written back into the backing database.

getNewId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping

getNewIds(InterMineObject, ObjectStore) - Method in interface org.intermine.api.bag.IdUpgrader

For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.

getNewIds(InterMineObject, ObjectStore) - Method in class org.intermine.web.bag.PkQueryIdUpgrader

For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.

getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService

Calculate the type of the new list.

getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService

getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListUploadService

getNewObject() - Method in class org.intermine.api.bag.ConvertedObjectPair

Get the newObject that was passed to the constructor.

getNewpassword() - Method in class org.intermine.web.struts.ChangePasswordForm

The new password

getNewpassword() - Method in class org.intermine.web.struts.PasswordResetForm

Gets the value of newpassword.

getNewpassword2() - Method in class org.intermine.web.struts.ChangePasswordForm

New password verification

getNewpassword2() - Method in class org.intermine.web.struts.PasswordResetForm

Gets the value of newpassword2.

getNewsPreview(String) - Static method in class org.intermine.dwr.AjaxServices

Work as a proxy for fetching remote file (RSS)

getNewTemplateQuery() - Method in class org.intermine.api.profile.TemplateQueryUpdate

getNewWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Create an ObjectStoreWriter that writes into this ObjectStore.

getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Create an ObjectStoreWriter that writes into this ObjectStore.

getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Create an ObjectStoreWriter that writes into this ObjectStore.

getNewWriter() - Method in interface org.intermine.objectstore.ObjectStore

Create an ObjectStoreWriter that writes into this ObjectStore.

getNewWriter() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Create an ObjectStoreWriter that writes into this ObjectStore.

getNewWriter() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Create an ObjectStoreWriter that writes into this ObjectStore.

getNextLine() - Method in class org.intermine.webservice.client.results.ResultSet

Get the next line of results.

getNextLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag

getNicerDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer

A JSP wants a nice name to display while the Displayer is loading

getNoConstraintsString() - Method in class org.intermine.pathquery.Path

Required for jsp

getNonXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

used for testing

getNoResultsMessage() - Method in class org.intermine.web.tags.table.TableTag

getNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject

getNoseyObjectStore(ObjectStore) - Method in class org.intermine.dataloader.BatchingFetcher

Returns an ObjectStore layered on top of the given ObjectStore, which reports to this fetcher which objects are being loaded.

getNotAnalysed() - Method in class org.intermine.web.logic.widget.HTMLWidget

getNotAnalysed() - Method in class org.intermine.web.logic.widget.Widget

getNote() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Note field from the attributes of this record.

getNullAttributes(String) - Method in class org.intermine.objectstore.ObjectStoreSummary

Get a list of the attributes that, for a given class, are always null or empty.

getNullConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the null/not null constraint value.

getNullConstraint() - Method in class org.intermine.web.struts.TemplateForm

Get the nullConstraint

getNullConstraint(String) - Method in class org.intermine.web.struts.TemplateForm

Get a nullConstraint

getNullReferencesAndCollections(String) - Method in class org.intermine.objectstore.ObjectStoreSummary

Get a list of the reference and collection names that, for a given class, are always null or empty.

getNumberOfBins() - Static method in class org.intermine.api.query.MainHelper.SummaryConfig

Returns the number of bins to split a histogram into.

getNumberOfMainTitlesToShow() - Method in class org.intermine.web.logic.config.HeaderConfigTitle

getNumberOfTableRowsToShow() - Method in class org.intermine.web.logic.results.ReportObject

The said function will resolve the maximum number of rows to show (in Collections) from webProperties.

getNumberOpt() - Method in class org.intermine.web.struts.WidgetForm

getNumericSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService

Get a summary for the values in column of a query.

getOAuth2Providers(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the set of accepted Open-ID providers.

getObject() - Method in class org.intermine.api.lucene.KeywordSearchHit

object

getObject() - Method in interface org.intermine.api.results.ResultCell

getObject() - Method in class org.intermine.api.results.ResultElement

Return the Object contained in this result element.

getoBJECT() - Method in interface org.intermine.model.InterMineObject

Returns the NotXml serialised version of this object.

getObject() - Method in class org.intermine.objectstore.proxy.ProxyReference

Gets the real object from the database.

getoBJECT() - Method in class org.intermine.objectstore.proxy.ProxyReference

Returns the NotXml serialised version of this object.

getObject() - Method in class org.intermine.objectstore.query.ContainsConstraint

Returns the InterMineObject of the constraint.

getObject() - Method in class org.intermine.web.logic.config.InlineListObject

Fetch the InterMine object (if needed)

getObject() - Method in class org.intermine.web.logic.results.DisplayReference

Get the referenced object

getObject() - Method in class org.intermine.web.logic.results.ReportObject

Get InterMine object

getObject() - Method in class org.intermine.web.logic.TreeNode

Get the Object

getObject() - Method in class org.intermine.web.search.KeywordSearchResult

returns original intermine object

getObject() - Method in class org.intermine.webservice.server.core.TableCell

getObjectByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

getObjectByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore

Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.

getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.

getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

getObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Search database for object matching the given object id

getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Search database for object matching the given object id and class

getObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore

Get an object from the ObjectStore by giving an ID.

getObjectById(Integer, Class<? extends InterMineObject>) - Method in interface org.intermine.objectstore.ObjectStore

Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.

getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get an object from the ObjectStore by giving an ID.

getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.

getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get an object from the ObjectStore by giving an ID.

getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.

getObjectHits - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

getObjectId() - Method in class org.intermine.web.logic.results.InlineResultsTableRow

Used from JSP

getObjectId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

Get the object id for this trail element.

getObjectIds(BrowseHit[]) - Static method in class org.intermine.api.lucene.KeywordSearch

getObjectOps - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

getObjectPrefetches - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

getObjects() - Method in class org.intermine.api.beans.PartnerLink

getObjects(InterMineAPI, Set<Integer>) - Static method in class org.intermine.api.data.Objects

Resolve a set of ids to mapping from ID to object.

getObjects() - Method in class org.intermine.webservice.client.results.JSONResult

getObjectsByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

getObjectsByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore

Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.

getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

getObjectsByIds(Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Get an objects from the ObjectStore that have the IDs in the ids colection

getObjectsByIds(Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStore

Get an objects from the ObjectStore that have the IDs in the ids colection

getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Get an objects from the ObjectStore that have the IDs in the ids colection

getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Get an objects from the ObjectStore that have the IDs in the ids colection

getObjectStore() - Method in interface org.intermine.api.API

getObjectStore() - Method in class org.intermine.api.InterMineAPI

getObjectStore() - Static method in class org.intermine.api.query.PathQueryAPI

Returns the production ObjectStore configured in webapp.os.alias.

getObjectStore() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Retrieve this Writer's ObjectStore.

getObjectStore() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Retrieve this Writer's ObjectStore.

getObjectStore() - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer

Returns the ObjectStore that this ParallelPrecomputer uses.

getObjectStore(String) - Static method in class org.intermine.objectstore.ObjectStoreFactory

Return an ObjectStore configured using properties

getObjectStore() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Retrieve this Writer's ObjectStore.

getObjectStore() - Method in interface org.intermine.objectstore.proxy.Lazy

Returns the ObjectStore that this lazy object will use

getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Returns the ObjectStore that this proxy will use

getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyReference

Returns the ObjectStore that this proxy will use

getObjectStore() - Method in class org.intermine.objectstore.query.ClobAccess

Returns the ObjectStore that this object will use to access data.

getObjectStore() - Method in class org.intermine.objectstore.query.PendingClob

Returns the ObjectStore that this object will use to access data.

getObjectStore() - Method in class org.intermine.objectstore.query.Results

Returns the ObjectStore that this Results object will use

getObjectStore() - Method in class org.intermine.objectstore.query.ResultsBatches

Returns the ObjectStore that this ResultsBatches object will use

getObjectStoreSummary() - Method in interface org.intermine.api.API

getObjectStoreSummary() - Method in class org.intermine.api.InterMineAPI

getObjectStoreWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Returns the underlying ObjectStoreWriter.

getObjectStoreWriter(String) - Static method in class org.intermine.objectstore.ObjectStoreWriterFactory

Return an ObjectStoreWriter configured using properties file

getObjectStoreWriter() - Method in class org.intermine.postprocess.PostProcessor

Return the ObjectStoreWriter that was passed to the constructor.

getObjectSummaryFields() - Method in class org.intermine.web.logic.results.ReportObject

A listing of object fields as pieced together from the various ReportObject methods

getObjectTagNames(String, String, String) - Method in class org.intermine.api.profile.TagManager

Returns names of tagged tags for specified object.

getObjectTagNames(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager

Returns names of tagged tags for specified object.

getObjectTags(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager

Get the tags for a specific object.

getObjectTags(String, String) - Static method in class org.intermine.dwr.AjaxServices

Returns all tags by which is specified object tagged.

getOboRelations() - Method in class org.intermine.bio.ontology.OboParser

getOboTerms() - Method in class org.intermine.bio.ontology.OboParser

getOfficialName(Connection, Integer) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for data from the applied_protocol_data table.

getOffset() - Method in class org.intermine.objectstore.query.ClobAccess

Return the offset into the underlying clob that this object is using.

getOffset() - Method in class org.intermine.objectstore.query.PendingClob

Return the offset into the underlying clob that this object is using.

getOffset() - Method in class org.intermine.sql.precompute.LimitOffsetQuery

Getter for offset.

getOffset() - Method in class org.intermine.sql.query.Query

Gets the OFFSET number for this query.

getOffsetConstraint(Query, QueryOrderable, Object, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Create a constraint to add to the main query to deal with offset - this is based on the first element in the order by (field) and a given value (x).

getOldId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping

getOldObject() - Method in class org.intermine.api.bag.ConvertedObjectPair

Get the objObject that was passed to the constructor.

getOldpassword() - Method in class org.intermine.web.struts.ChangePasswordForm

The old password

getOnClick() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

getOntology(DataConverter) - Static method in class org.intermine.bio.util.BioConverterUtil

Create and store ontology object.

getOntologyTerm() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the OntologyTerm field from the attributes of this record.

getOp() - Method in class org.intermine.objectstore.query.Constraint

Get op of constraint

getOp() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

Returns the op of this combination.

getOp() - Method in class org.intermine.pathquery.PathConstraint

Returns the operation that this constraint performs.

getOp() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Get a string representation of the constraint operation.

getOpened() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Returns true if disclosure is opened else false.

getOpenIdProviders(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the set of accepted Open-ID providers.

getOperands() - Method in class org.intermine.sql.query.Function

Returns the List of operands of this function.

getOperation() - Method in class org.intermine.objectstore.query.QueryExpression

Returns the operation.

getOperation() - Method in class org.intermine.objectstore.query.QueryFunction

Returns the operation of the function.

getOperation() - Method in class org.intermine.sql.query.Constraint

Returns the operation of the constraint.

getOperation() - Method in class org.intermine.sql.query.Function

Returns the operation of the function.

getOperation() - Method in class org.intermine.template.TemplateValue

getOperation() - Method in class org.intermine.webservice.client.template.TemplateParameter

getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListDifferenceService

getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListIntersectionService

getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService

Get the BagOperation that will create the list.

getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListSubtractionService

getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListUnionService

getOperationButton() - Method in class org.intermine.web.struts.SaveBagForm

getOperationCode() - Method in class org.intermine.api.bag.operations.BagOperation

getOperationCode() - Method in class org.intermine.api.bag.operations.Intersection

getOperationCode() - Method in class org.intermine.api.bag.operations.RelativeComplement

getOperationCode() - Method in class org.intermine.api.bag.operations.SymmetricDifference

getOperationCode() - Method in class org.intermine.api.bag.operations.Union

getOperator() - Method in class org.intermine.pathquery.LogicExpression.And

Override to provide text symbol for this operator.

getOperator() - Method in class org.intermine.pathquery.LogicExpression.Operator

Override to provide text symbol for this operator.

getOperator() - Method in class org.intermine.pathquery.LogicExpression.Or

Override to provide text symbol for this operator.

getOperator() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the operator.

getOptimised() - Method in class org.intermine.sql.precompute.OptimiserCacheLine

Gets the optimised query (minus the LIMIT and OFFSET) from this cache line.

getOptionalParameter(String, String) - Method in class org.intermine.webservice.server.WebService

Get a parameter this service deems to be optional, or the default value.

getOptionalParameter(String) - Method in class org.intermine.webservice.server.WebService

Get a parameter this service deems to be optional, or null.

getOptions() - Method in class org.intermine.web.task.IssueTokenTask

getOptions() - Method in class org.intermine.web.task.KeyStoreTask

Get the options as configured for this task

getOptionsTileName() - Method in class org.intermine.web.logic.config.TableExportConfig

Get the optionsTileName of this TableExportConfig - ie. the tile to be inserted into the export options page for this type of export.

getOrderBy() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getOrderBy() - Method in class org.intermine.objectstore.query.Query

Gets the ORDER BY clause of this Query

getOrderBy() - Method in class org.intermine.pathquery.PathQuery

Returns the current order by list.

getOrderBy() - Method in class org.intermine.sql.query.Query

Gets the list of fields forming the ORDER BY clause of this query.

getOrderByAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getOrderByField() - Method in class org.intermine.sql.precompute.PrecomputedTable

Returns the name of the order by field, if it exists.

getOrderPath() - Method in class org.intermine.pathquery.OrderElement

Returns the path of this OrderElement.

getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

The Organism item created from the taxon id passed to the constructor.

getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter

The Organism item created from the taxon id passed to the constructor.

getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Get and store() the Organism object to reference when creating new objects.

getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return the organism Item created for this GFF3Converter from the organism abbreviation passed to the constructor.

getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the organism Item set by setOrganism()

getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.UniProtFastaLoaderTask

Get and store() the Organism object to reference when creating new objects.

getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return some SQL that can be included in the WHERE part of query that restricts features by organism.

getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.StockProcessor

Return some SQL that can be included in the WHERE part of query that restricts features by organism.

getOrganismDataByAbbreviation(String) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by abbreviation, abbreviations are not case sensitive.

getOrganismDataByFullName(String) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by a full name that is genus species.

getOrganismDataByGenusSpecies(String, String) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by genus and species - both must match.

getOrganismDataByShortName(String) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by shortName, short names are case sensitive.

getOrganismDataByTaxon(int) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by taxon id.

getOrganismDataByTaxonInternal(int) - Method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by taxon id.

getOrganismDataByUniprot(String) - Static method in class org.intermine.bio.util.OrganismRepository

Look up OrganismData objects by Uniprot abbreviation, eg HUMAN or DROME.

getOrganismItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter

The Organism item created from the taxon id passed to the constructor.

getOrganismRepository() - Static method in class org.intermine.bio.util.OrganismRepository

Return an OrganismRepository created from a properties file in the class path.

getOrganisms(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

Retrieve the organisms to be updated

getOrganisms(ObjectStore, String, List<Integer>, boolean) - Static method in class org.intermine.bio.util.BioUtil

For a bag of objects, returns a list of organisms

getOrganisms(ObjectStore, String, List<Integer>, boolean, String) - Static method in class org.intermine.bio.util.BioUtil

For a bag of objects, returns a list of organisms.

getOrganismsToProcess() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Return the OrganismData objects for the organisms listed in the source configuration.

getOrig() - Method in class org.intermine.dataloader.ObjectDescription

Returns the original data, as reflected in the backing database.

getOrigin() - Method in class org.intermine.api.search.OriginatingEvent

Get the web searchable involved in this event.

getOriginal() - Method in class org.intermine.sql.precompute.OptimiserCacheLine

Returns the original SQL string.

getOriginalSql() - Method in class org.intermine.sql.precompute.PrecomputedTable

Returns the original SQL text stored in the index for this PrecomputedTable

getOriginalValue() - Method in class org.intermine.web.logic.query.DisplayConstraint

getOrigType() - Method in class org.intermine.web.logic.query.MetadataNode

Returns the type of this node if it did not have a subclass constraint.

getOs() - Method in class org.intermine.objectstore.query.ClobAccess

Returns the ObjectStore that this object uses.

getOsb() - Method in class org.intermine.api.profile.InterMineBag

Returns the ObjectStoreBag, so that elements can be added and removed.

getOsb() - Method in class org.intermine.api.profile.InvalidBag

getOsb() - Method in class org.intermine.api.profile.StorableBag

Return a reference to the object store bag contained in the production database.

getOsb() - Method in class org.intermine.objectstore.query.BagConstraint

Get the ObjectStoreBag.

getOsb() - Method in class org.intermine.objectstore.query.QueryClassBag

Returns the ObjectStoreBag.

getOsName() - Method in class org.intermine.task.ConverterTask

Return the object store alias set by setOsName().

getOuterInSummary() - Method in class org.intermine.web.logic.config.FieldConfig

getOuterJoinGroup() - Method in class org.intermine.pathquery.Node

Returns a String describing the outer join group that this Node is in.

getOuterJoinGroup(String) - Static method in class org.intermine.pathquery.Node

Returns a String describing the outer join group that the given path string is in.

getOuterJoinGroup(String) - Method in class org.intermine.pathquery.PathQuery

Returns the outer join group that the given path is in.

getOuterJoinGroups() - Method in class org.intermine.pathquery.PathQuery

Returns the outer join groups map for this query, if the query verifies correctly.

getOuterJoinStatus(String) - Method in class org.intermine.pathquery.PathQuery

Returns the outer join status of the last part of a given path in this query.

getOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery

Returns an unmodifiable Map which is a copy of the current outer join status of this query at the time of execution of this method.

getOuterMap() - Method in class org.intermine.pathquery.PathQuery

Returns a Map from path to TRUE for all paths that are outer joined.

getOutputInfo(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Return the key value pairs to put in the webservice result

getOutsideOptions() - Method in class org.intermine.api.query.range.AbstractHelper

By default the OUTSIDE options are the negation of the WITHIN options, with the right and left fields swapped.

getOutwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil

Creates a column name for the "outward" key of a many-to-many collection descriptor.

getOverlapsOptions() - Method in class org.intermine.api.query.range.AbstractHelper

By default the OVERLAPS options are the same as the WITHIN options with the right and left fields swapped.

getPackageName() - Method in class org.intermine.objectstore.query.iql.IqlQuery

Get the package name

getPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the page index.

getPagedTable() - Method in class org.intermine.web.logic.query.PageTableQueryMonitor

Return the PagedTable that was passed to the constructor.

getPagedTable(HttpServletRequest, HttpSession) - Method in class org.intermine.web.struts.TableExportAction

getPageLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag

getPageName() - Method in class org.intermine.web.struts.ModifyBagForm

getPageName() - Method in class org.intermine.web.struts.ModifyTemplateForm

getPageSize() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the page size of the current page

getPageSize() - Method in class org.intermine.web.struts.ChangeTableSizeForm

Get the page size

getPageSize() - Method in class org.intermine.web.tags.table.NavigationBarTag

getParam() - Method in class org.intermine.objectstore.query.QueryFunction

Returns the QueryEvaluable of the function.

getParam2() - Method in class org.intermine.objectstore.query.QueryFunction

Returns the second evaluable, where these is one.

getParameter(String) - Method in interface org.intermine.webservice.client.core.Request

Use only if you are sure, that the parameter has only one value else use getParameterValues method.

getParameter(String) - Method in class org.intermine.webservice.client.core.RequestImpl

Use only if you are sure, that the parameter has only one value else use getParameterValues method.

getParameterJson() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the parameters for this displayer as a JSONObject

getParameterMap() - Method in interface org.intermine.webservice.client.core.Request

Returns all parameters as an unmodifiable map.

getParameterMap() - Method in class org.intermine.webservice.client.core.RequestImpl

Returns all parameters as an unmodifiable map.

getParameterName() - Method in class org.intermine.web.logic.template.ConstraintInput

getParameterNames() - Method in interface org.intermine.webservice.client.core.Request

getParameterNames() - Method in class org.intermine.webservice.client.core.RequestImpl

getParameters() - Method in class org.intermine.objectstore.query.iql.IqlQuery

Get the parameters

getParameters() - Method in class org.intermine.web.util.AttributeLinkURL

getParameterString() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

A JSON string representing custom parameters for this displayer.

getParameterValues(String) - Method in interface org.intermine.webservice.client.core.Request

getParameterValues(String) - Method in class org.intermine.webservice.client.core.RequestImpl

getParams() - Method in class org.intermine.web.logic.config.Displayer

Return the parameters stored in this Displayer.

getParent() - Method in class org.intermine.objectstore.query.OverlapRange

Returns the parent parameter.

getParent() - Method in class org.intermine.pathquery.Node

Get the parent node.

getParent() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns a new DisplayPath that represents the parent path, or null if this path is just a root class.

getParentId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Get parentId value

getParents() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the list of the Parent field from the attributes of this record.

getParentTermId() - Method in class org.intermine.bio.ontology.OboRelation

getParentType() - Method in class org.intermine.pathquery.Node

Type of parent node.

getParentType() - Method in class org.intermine.web.logic.results.InlineResultsTable

Get the parent's type

getPartialString(List<String>) - Method in class org.intermine.pathquery.LogicExpression

Produce an expression for this branch of the tree displaying only the children containing the variable in input

getParts() - Method in class org.intermine.webservice.client.core.MultiPartRequest

getPassword() - Method in class org.intermine.api.profile.Profile

Get the value of password

getPassword(String) - Method in class org.intermine.api.profile.ProfileManager

Get a user's password A check should be made prior to this call to ensure a Profile exists

getPassword() - Method in class org.intermine.sql.Database

Gets the password for this Database

getPassword() - Method in class org.intermine.web.struts.CreateAccountForm

getPassword() - Method in class org.intermine.web.struts.LoginForm

Gets the value of password

getPassword() - Method in class org.intermine.webservice.server.WebServiceInput

getPassword2() - Method in class org.intermine.web.struts.CreateAccountForm

getPath() - Method in class org.intermine.api.results.Column

Get the Path set by setPath().

getPath() - Method in interface org.intermine.api.results.ResultCell

getPath() - Method in class org.intermine.api.results.ResultElement

getPath() - Method in class org.intermine.pathquery.PathConstraint

Returns the path that this constraint is attached to.

getPath() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart

The path that should be in the title, with style removed.

getPath() - Method in class org.intermine.web.logic.config.InlineListConfig

getPath() - Method in class org.intermine.web.logic.query.DisplayConstraint

Get a representation of the path that is being constraint.

getPath() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Return the underlying path object.

getPath() - Method in class org.intermine.web.logic.results.InlineList

getPath() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of path

getPath() - Method in class org.intermine.webservice.server.core.TableCell

getPathConstraint() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

Returns the pathConstraint based on the enrichmentIdentifier will be applied on the pathQUery

getPathConstraints() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getPathConstraintsForView() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getPathId() - Method in class org.intermine.web.logic.template.ConstraintInput

getPathId() - Method in class org.intermine.webservice.client.template.TemplateParameter

getPathQuery() - Method in class org.intermine.api.profile.SavedQuery

Get the saved PathQuery.

getPathQuery() - Method in class org.intermine.api.results.WebResults

getPathQuery() - Method in interface org.intermine.api.results.WebTable

Get the PathQuery associated with this WebTable

getPathQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

getPathQuery() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getPathQuery() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.

getPathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget

Returns the pathquery based on the views set in config file and the bag constraint.

getPathQuery() - Method in class org.intermine.web.logic.widget.HTMLWidget

getPathQuery() - Method in class org.intermine.web.logic.widget.TableWidget

getPathQuery() - Method in class org.intermine.web.logic.widget.Widget

Return the PathQuery generated dynamically by the attribute views in the configuration file

getPathQueryExecutor(Profile) - Method in interface org.intermine.api.API

getPathQueryExecutor() - Method in class org.intermine.api.InterMineAPI

getPathQueryExecutor(Profile) - Method in class org.intermine.api.InterMineAPI

getPathQueryExecutor() - Static method in class org.intermine.api.query.PathQueryAPI

Returns a PathQueryExecutor, using properties.

getPathQueryForMatches() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

Returns the pathquery based on the startClassDisplay, constraintsForView set in config file and the bag constraint Executed when the user click on the matches column in the enrichment widget.

getPathsString() - Method in class org.intermine.web.struts.TableExportForm

Get the paths string in the format: "Class.field Class.field2 Class.ref.field"

getPathString() - Method in class org.intermine.pathquery.Node

Gets the String value of pathString of this node (eg.

getPathString() - Method in exception org.intermine.pathquery.PathException

Return the path String that was passed to the constructor.

getPathString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns the full path string for this path.

getPathString() - Method in class org.intermine.web.logic.results.ReportObjectField

Get a path string to fetch field descriptions

getPathStrings() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

Comma separated list of path strings to appear in the widget, ie Employee.firstName, Employee.lastName

getPathToBagQueryResult() - Method in class org.intermine.api.results.WebResults

Returns the pathToBagQueryResult Map.

getPathToBagQueryResult() - Method in interface org.intermine.api.results.WebTable

Returns the pathToBagQueryResult Map.

getPathToIndex() - Method in class org.intermine.api.results.WebResults

Create a map from string paths to index of QueryNodes in the ObjectStore query

getPathToQueryNode() - Method in class org.intermine.api.results.WebResults

Returns the pathToQueryNode Map.

getPathUpdated(String, Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate

Update the path given in input with the renamed classes and fields

getPathWithoutSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil

getPerlWSModuleVer() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getPermanentBaseURL() - Method in class org.intermine.web.util.URLGenerator

Generates base url.

getPermission(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Get the level of permission granted by an access token.

getPermission(PermanentToken, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

getPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Authenticate a user using username/password credentials.

getPermission() - Method in class org.intermine.webservice.server.WebService

Return the permission object representing the authorisation state of the request.

getPhase() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the phase field of this record.

getPlacement() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the data category name under which this displayer should appear.

getPlatform() - Method in class org.intermine.sql.Database

Gets the platform of this Database

getPoints() - Method in class org.intermine.web.search.KeywordSearchResult

return points

getPopularTemplatesByAspect(String, Integer) - Method in class org.intermine.api.template.TemplateManager

Return the template list for a particular aspect given in input, ordered by rank descendant

getPopularTemplatesByAspect(String, Integer, String, String) - Method in class org.intermine.api.template.TemplateManager

Return the template list for a particular aspect, ordered by rank descendant for the user/sessionid specified in the input

getPopulatedTemplate(TemplateQuery, Map<String, List<TemplateValue>>) - Static method in class org.intermine.api.template.TemplatePopulator

Given a template and a map of values for editable constraints on each editable node create a copy of the template query with the values filled in.

getPopulationBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

Get the bag's name for reference population

getPopulationInfo() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

Return a population info instance contanining the population size, N (In our example this is the total number of companies, or possibly the total number of companies that have at least one Department) and the average length of the genes in the whole population.

getPopulationInfo() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getPopulationQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

getPossibleValues(ApiTemplate, String) - Method in class org.intermine.api.template.TemplateSummariser

Returns the possible values that a particular path in a template query can take, for dropdowns on template forms.

getPossibleValues(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser

Returns a Map of the possible values for editable nodes on a template query.

getPossibleValues() - Method in class org.intermine.web.logic.query.DisplayConstraint

Values to populate a dropdown for the path if possible values are available.

getPrecomputedSummarisedInfo(Profile, HttpSession, HttpServletRequest) - Static method in class org.intermine.web.struts.MyMineController

Retrieve the information about precomputed and summarised templates for the given profile, and store it into the request

getPrecomputedTables() - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Get all the precomputed tables in the underlying database.

getPrecomputeQuery(TemplateQuery, List) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper

Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.

getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper

Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.

getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String, InterMineAPI) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper

Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.

getPrecomputer(ObjectStoreInterMineImpl) - Method in class org.intermine.task.PrecomputeTask

Create a ParallelPrecomputer.

getPrecomputeTemplateQueries() - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Get the super user's public templates

getPreDefaultBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig

Return a List of BagQuerys for the given type that should be run before the default query

getPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager

getPreferences() - Method in class org.intermine.api.profile.Profile

Get the object representing the preferences of this user.

getPreferences(Profile) - Method in class org.intermine.api.profile.ProfileManager

Get the preferences for a profile.

getPrefix() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

getPrefix() - Method in class org.intermine.pathquery.Node

Gets the value of prefix

getPrefix() - Method in class org.intermine.pathquery.Path

Return a Path object that represents the prefix of this path, ie this Path without the last element.

getPrefix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart

A prefix that may be an HTML tag to appear before this part in the title.

getPrefix() - Method in class org.intermine.web.logic.results.InlineList

getPrefixes() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

used for testing

getPreviousLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag

getPrimaryAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getPrimaryIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getPrimaryKeys(ClassDescriptor, Source, ObjectStore) - Static method in class org.intermine.dataloader.DataLoaderHelper

Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor.

getPrintWriterForClient(HttpServletRequest, OutputStream) - Static method in class org.intermine.web.logic.export.http.HttpExportUtil

getPriorities(Class<? extends FastPathObject>, String) - Method in class org.intermine.dataloader.PriorityConfig

Returns a List of data source names representing the priority for a given class and fieldname pair.

getProblems() - Method in exception org.intermine.api.query.codegen.InvalidQueryException

getProcessingInstruction() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getProcessingInstruction() - Method in class org.intermine.webservice.server.output.XMLFormatter

getProcessor() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

getProcessor() - Method in class org.intermine.webservice.server.widget.GraphService

getProcessor() - Method in class org.intermine.webservice.server.widget.TableWidgetService

getProcessor() - Method in class org.intermine.webservice.server.widget.WidgetService

getProductionObjectStore() - Method in class org.intermine.api.profile.ProfileManager

Return the ObjectStore that was passed to the constructor.

getProfile() - Method in class org.intermine.api.bag.operations.BagOperation

getProfile() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

getProfile(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Get a user's Profile using a username, password and the classKeys.

getProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager

Get a user's Profile using a username and password.

getProfile(String) - Method in class org.intermine.api.profile.ProfileManager

Get a user's Profile using a username

getProfile(int) - Method in class org.intermine.api.profile.ProfileManager

Get a user's Profile using an ID

getProfile(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Get a user's Profile using a username

getProfile() - Static method in class org.intermine.api.query.PathQueryAPI

Returns the superuser Profile.

getProfile() - Method in class org.intermine.api.search.SearchRepository

Get the profile that this repository belongs to.

getProfile(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns user profile saved in session.

getProfile() - Method in class org.intermine.webservice.server.user.DeletionToken

getProfileId() - Method in class org.intermine.api.profile.StorableBag

getProfileManager() - Method in interface org.intermine.api.API

getProfileManager() - Method in class org.intermine.api.InterMineAPI

getProfileManager() - Method in class org.intermine.api.profile.Profile

Return the ProfileManager that was passed to the constructor.

getProfileManager() - Static method in class org.intermine.api.query.PathQueryAPI

Returns the ProfileManager configured in webapp.userprofile.os.alias.

getProfileObjectStoreWriter() - Method in class org.intermine.api.profile.ProfileManager

Return the userprofile ObjectStoreWriter that was passed to the constructor.

getProfileUserName(int) - Method in class org.intermine.api.profile.ProfileManager

Return the name of the user with the given internal DB id.

getProfileUserNames() - Method in class org.intermine.api.profile.ProfileManager

Return a List of the usernames in all of the stored profiles.

getProjects(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the project name.

getProjectTitle() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getProperties() - Static method in class org.intermine.api.query.PathQueryAPI

Returns the properties accessible for this system.

getProperties() - Static method in class org.intermine.util.PropertiesUtil

Returns all InterMine properties

getProperties() - Method in class org.intermine.webservice.client.results.Item

Return a view of the properties in this row.

getPropertiesFileName(String) - Static method in class org.intermine.task.PrecomputeTask

Return the name of the properties file we will read.

getPropertiesOrigins(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Gets the origins map from the servlet context.

getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.util.PropertiesUtil

Returns all Properties in props that begin with str

getPropertiesStartingWith(String) - Static method in class org.intermine.util.PropertiesUtil

Returns all global Properties that begin with str

getProperty(String, String) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

Get a configured property for which an accessor does not exist.

getProperty() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption

Get the constraint index to be put in form when this op is selected.

getProperty(String) - Method in class org.intermine.webservice.server.WebService

Get a configuration property by name.

getPropertyDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo

getPropertyDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo

getPropertyName() - Method in class org.intermine.web.struts.EditPropertiesForm

getPropertyValue() - Method in class org.intermine.web.struts.EditPropertiesForm

getProteinNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry

if an isoform has two ID tags, then the first one is used and the second one is added as a synonym

getProtocolAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for protocols from the attribute table.

getProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed from the protocol table.

getProvider() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

getPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return a ReferenceList containing the Publication Items ids set by addPublication()

getPublications(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Retrieve the publications to be updated

getPublicId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput

Returns id of object.

getPublicTagNames(ClassDescriptor) - Method in class org.intermine.api.profile.TagManager

Get all the tags that all users have access to.

getPublicTagNames(Taggable) - Method in class org.intermine.api.profile.TagManager

Get all the tags that all users have access to.

getPublicTagNames(String, String) - Method in class org.intermine.api.profile.TagManager

Get the tags for an object that are visible to all users.

getPubRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

getPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the pub table.

getPubs() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getPValue() - Method in class org.intermine.web.struts.WidgetForm

getPValues() - Method in class org.intermine.web.logic.widget.EnrichmentResults

Get the probability of enrichment for each attribute value found in the sample.

getQcb() - Method in class org.intermine.objectstore.query.QueryCollectionReference

Gets the QueryClassBag of this QueryReference.

getQcObject() - Method in class org.intermine.objectstore.query.QueryCollectionReference

Gets the InterMineObject of this QueryReference.

getQcType() - Method in class org.intermine.objectstore.query.QueryCollectionReference

Returns the type of the queryclass of this reference

getQcType() - Method in class org.intermine.objectstore.query.QueryReference

Returns the type of the queryclass of this reference

getQope() - Method in class org.intermine.objectstore.query.PathExpressionField

Returns the QueryObjectPathExpression.

getQualifiedType() - Method in class org.intermine.api.profile.InterMineBag

Get the fully qualified type of this bag

getQueried(String) - Method in class org.intermine.dataloader.EquivalentObjectHints

Returns a Set of values that have been tested for a particular class and fieldname.

getQueries() - Method in class org.intermine.sql.precompute.BestQueryStorer

Gets the set of queries added to this object

getQuery(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery

Return the Query that was passed to the constructor.

getQuery() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore

getQuery(String) - Method in interface org.intermine.api.query.QueryStore

getQuery() - Method in class org.intermine.api.results.ExportResultsIterator

getQuery() - Method in interface org.intermine.objectstore.proxy.LazyCollection

Returns the Query used by this LazyCollection

getQuery() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Returns the Query used by this LazyCollection

getQuery(Collection<? extends InterMineObject>) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.

getQuery(Collection<Integer>, boolean) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.

getQuery() - Method in class org.intermine.objectstore.query.Results

Get the Query that produced this Results object.

getQuery() - Method in class org.intermine.objectstore.query.ResultsBatches

Get the Query that produced this ResultsBatches object.

getQuery() - Method in class org.intermine.objectstore.query.SubqueryConstraint

Get the query.

getQuery() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint

Get the query.

getQuery() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass

Returns the query.

getQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Returns the Query of this Candidate, converting from a String if necessary.

getQuery() - Method in class org.intermine.sql.precompute.LimitOffsetQuery

Getter for the stripped query.

getQuery() - Method in class org.intermine.sql.precompute.PrecomputedTable

Gets the Query that is materialised in this PrecomputedTable

getQuery() - Method in class org.intermine.sql.query.SubQuery

Returns the query contained in the subquery.

getQuery() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor

Return the Query that was passed to the constructor.

getQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns the PathQuery on the session.

getQuery(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns the PathQuery on the session.

getQuery(String, List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

Returns the relevant query.

getQuery(boolean, List<String>) - Method in class org.intermine.web.logic.widget.TableWidgetLdr

getQuery() - Method in class org.intermine.web.struts.QueryForm

getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.query.QueryToListService

Get the pathquery to use for this request.

getQuery(PathQuery, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService

Get the Objectstore Query to run to generate the list.

getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilder

Returns parsed PathQuery.

getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj

For the purposes of exporting into JSON objects the view must be: Ordered by length, such that Company.departments.name precedes Company.departments.employees.name Be constituted so that every class has an attribute on it, root class included, and every reference along the way.

getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.template.TemplateToListService

getQueryBuilder() - Method in class org.intermine.web.struts.ImportQueriesForm

Get the queryBuilder field.

getQueryBuilder(String) - Method in class org.intermine.webservice.server.query.AbstractQueryService

Get a path-query builder.

getQueryClass() - Method in class org.intermine.objectstore.query.ContainsConstraint

Returns the QueryClass of the constraint.

getQueryClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the QueryClass of which the field is a member.

getQueryClass() - Method in class org.intermine.objectstore.query.QueryForeignKey

Gets the QueryClass of which this reference is an member.

getQueryClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the QueryClass of which the field is a member.

getQueryClass() - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect

Returns the QueryClass of which the field is a member.

getQueryClass() - Method in class org.intermine.objectstore.query.QueryReference

Gets the QueryClass of which this reference is an member.

getQueryClass() - Method in class org.intermine.objectstore.query.SubqueryConstraint

Get the QueryClass the query is compare with

getQueryDesc() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult

getQueryEvaluable() - Method in class org.intermine.objectstore.query.SubqueryConstraint

Get the QueryEvaluable the query is compared with

getQueryFields(QueryEvaluable) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Descends into QueryExpression and QueryFunction objects to find all instances of QueryField.

getQueryForWildcards(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery

Return a Query to fetch bag contents for wildcards.

getQueryInfo(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Retrieve an entry from the infoCache.

getQueryMap() - Method in class org.intermine.web.struts.ImportQueriesForm

Return a Map from query name to Query object.

getQueryMap(BagManager, Profile) - Method in class org.intermine.web.struts.TemplatesImportForm

Return a Map from template name to Template object.

getQueryName() - Method in class org.intermine.web.struts.SaveQueryForm

Get the query name

getQueryNode() - Method in class org.intermine.objectstore.query.BagConstraint

Get the QueryNode.

getQueryOrderable() - Method in class org.intermine.objectstore.query.OrderDescending

Return the encapsulated QueryOrderable.

getQueryService() - Method in class org.intermine.webservice.client.core.ServiceFactory

Return a new QueryService for getting query results from.

getQueryStore() - Method in class org.intermine.api.InterMineAPI

getQueryString() - Method in class org.intermine.objectstore.query.iql.IqlQuery

Get the query String NOTE: this will be unvalidated

getQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Returns the String query of this Candidate, converting from Query if necessary.

getQueryTime() - Method in class org.intermine.objectstore.intermine.ExtraQueryTime

Returns the total amount of time spent in extra queries, in milliseconds.

getQueryToExecute() - Method in class org.intermine.pathquery.PathQuery

Get the PathQuery that should be executed.

getQueryToExecute() - Method in class org.intermine.template.TemplateQuery

Fetch the PathQuery to execute for this template.

getQueryTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices

getQueryTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getQueryWithDefaultView(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Used for making a query for a reference or collection.

getQueryXml() - Method in class org.intermine.webservice.server.query.QueryRequestParser

Get query XML from a request.

getRangeConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the range constraint value.

getRangeLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Get the value of rangeLabel

getRangeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

getRangeQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the set of operators valid for range constraints.

getRanges() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

getRangeSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions

getRank(TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker

Return the rank for each public template.It represents a relationship between the templates executions; a template with rank 1 has been executed more than a template with rank 2.

getRank(TemplateManager) - Method in class org.intermine.api.tracker.TrackerDelegate

Return the rank associated to the templates

getRatDiseases(String) - Static method in class org.intermine.dwr.AjaxServices

Return list of disease ontology terms associated with list of provided rat genes.

getRatIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a rat id resolver

getRatIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a rat id resolver

getRatIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a rat id resolver

getRawOutput() - Method in class org.intermine.webservice.server.WebService

Get access to the underlying print-writer.

getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

Obtain the pubmed esummary information for the organisms

getReader(Integer) - Static method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Obtain the pubmed esummary information for the publications

getReader() - Method in class org.intermine.webservice.client.results.ResultSet

Get a reader over the data, for reading line-by-line.

getReader(HttpServletRequest) - Method in class org.intermine.webservice.server.lists.ListUploadService

Get the reader for the identifiers uploaded with this request.

getReason() - Method in exception org.intermine.webservice.client.exceptions.ResultException

Get the reason for this error.

getReference() - Method in class org.intermine.objectstore.query.ContainsConstraint

Returns the QueryReference of the constraint.

getReference(String) - Method in class org.intermine.webservice.client.results.Item

Get in Item representing the record referenced by a reference field.

getReference(String) - Method in class org.intermine.xml.full.Item

Get a named reference.

getReferenceLists() - Method in class org.intermine.webservice.server.lists.ListInput

getReferenceName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction

Return the referenceName that was passed to the constructor.

getReferences() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields

Returns the Set of references

getReferences() - Method in class org.intermine.xml.full.Item

Get all the references.

getRefId() - Method in class org.intermine.xml.full.Reference

Get the refId of this field

getRefIds() - Method in class org.intermine.xml.full.ReferenceList

Get the references in this collection.

getRefsAndCollections() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

getRefsAndCollections() - Method in class org.intermine.web.logic.results.ReportObject

Get all the reference and collection fields and values for this object

getRelationship() - Method in class org.intermine.bio.ontology.OboRelation

getRelease() - Static method in class org.intermine.web.filters.ReleaseEtagFilter

getRelease() - Method in class org.intermine.webservice.client.core.Service

getReleaseVersion() - Method in class org.intermine.api.mines.LocalMine

getReleaseVersion() - Method in interface org.intermine.api.mines.Mine

getReleaseVersion() - Method in class org.intermine.api.mines.RemoteMine

getRelevantConstraints() - Method in class org.intermine.pathquery.PathQuery

getRelevantConstraints() - Method in class org.intermine.template.TemplateQuery

getRenamedBags() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues

Get the mapping from old to new names.

getRenamedClasses() - Method in class org.intermine.api.profile.ModelUpdate

Return a map containing the couple previous class and new class

getRenamedFields() - Method in class org.intermine.api.profile.ModelUpdate

Return a map containing the couple previousClass.previuosField and new field

getRenamedTemplates() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues

Get the names of all the templates that failed.

getReplacedFieldExprs() - Method in class org.intermine.web.displayer.ReportDisplayer

Get a list of field names and paths that should be replaced by this displayer - i.e. this displayer should be shown instead of other fields.

getReplacedFieldExprs() - Method in class org.intermine.web.logic.results.ReportObject

Get fields and paths that are replaced by custom report displayers and should not be shown in the report page.

getReplacedFieldNames() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the names of fields this displayer replaces.

getReplacesFields() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the comma separated list of field names that should not be displayed on the report page when this displayer is used.

getReportDisplayer(String) - Method in class org.intermine.web.logic.results.ReportObject

Give us a displayer by a specific name, called by AjaxServices

getReportDisplayerByName(String, String) - Method in class org.intermine.web.displayer.DisplayerManager

Get a specific ReportDisplayer by its name for a given ReportObject type

getReportDisplayerConfigs() - Method in class org.intermine.web.logic.config.WebConfig

Fetch config for the report page displayers.

getReportDisplayers() - Method in class org.intermine.web.logic.results.ReportObject

Get a map from placement (header, summary or a data category) to custom report displayers for that placement.

getReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager

Get a map from placement string (a data category or summary) to displayers for the given type.

getReportObject(HttpSession, String) - Method in class org.intermine.web.struts.ModifyDetails

Get a ReportObject from the session given the object id as a string.

getReportObjects(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Return the ReportObjects Map from the session or create and return it if it doesn't exist.

getReportPageTemplatesForAspect(String, Set<String>) - Method in class org.intermine.api.template.TemplateManager

Get a list of template queries that should appear on report pages for the given type under the specified aspect.

getRequest() - Static method in class org.intermine.objectstore.query.PrefetchManager

Returns a request for a thread to service.

getRequestFileName() - Method in class org.intermine.webservice.server.WebService

If the request has a filename parameter then use that for the fileName, otherwise use the default fileName

getRequiredParameter(String) - Method in class org.intermine.webservice.server.WebService

Get a parameter this service deems to be required.

getResponseBodyAsStream() - Method in class org.intermine.webservice.client.util.HttpConnection

getResponseBodyAsString() - Method in class org.intermine.webservice.client.util.HttpConnection

Return the response body, ensuring that the connection is closed upon completion.

getResponseCode() - Method in class org.intermine.webservice.client.util.HttpConnection

getResponseHeader(String) - Method in class org.intermine.webservice.client.util.HttpConnection

getResponseStream() - Method in class org.intermine.webservice.client.util.HttpConnection

getResponseTable(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Performs the actual remote request and fetches the results.

getResponseType() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getResponseType() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getResponseType() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getResult() - Method in interface org.intermine.api.idresolution.Job

getResult() - Method in class org.intermine.api.idresolution.ResolutionJob

getResult() - Method in class org.intermine.api.idresolution.UpgradeJob

getResultElementRows() - Method in class org.intermine.web.logic.results.InlineResultsTable

Main method used from report to resolve a tablefull of ResultElements

getResultElements(int) - Method in class org.intermine.api.results.WebResults

Return a List containing a ResultElement object for each element in the given row.

getResultElements(int) - Method in interface org.intermine.api.results.WebTable

Return a List containing a ResultElement object for each element given in the given row.

getResultRows(PagedTable, HttpServletRequest) - Method in class org.intermine.web.logic.export.http.HttpExporterBase

getResults() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult

getResults() - Method in interface org.intermine.web.logic.widget.DataSetLdr

Get the Results object

getResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

getResults() - Method in class org.intermine.web.logic.widget.GraphWidget

getResults() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader

getResults() - Method in class org.intermine.web.logic.widget.HTMLWidget

getResults() - Method in class org.intermine.web.logic.widget.TableWidget

getResults() - Method in class org.intermine.web.logic.widget.Widget

Return the result that represents the data from this widget.

getResults() - Method in class org.intermine.webservice.client.results.JSONResult

getResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService

getResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Returns a specific set of the results of the specified PathQuery.

getResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Returns a set of the results for the given template template with the given parameters, defined by the index of the first result you want back, and the maximum page size.

getResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService

getResults() - Method in class org.intermine.webservice.server.output.MemoryOutput

Returns results added to output

getResultsAsList() - Method in class org.intermine.web.logic.results.InlineResultsTable

getResultsBatches() - Method in class org.intermine.objectstore.query.Results

Returns the underlying ResultsBatches object that this object is using, in order to create more Results objects (with different settings) from it.

getResultsCount() - Method in class org.intermine.webservice.server.output.MemoryOutput

}

getResultsCount() - Method in class org.intermine.webservice.server.output.Output

getResultsCount() - Method in class org.intermine.webservice.server.output.StreamedOutput

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONObjResultProcessor

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONResultProcessor

The method a processor must implement to produce a results iterator.

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONRowResultProcessor

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONSummaryProcessor

getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONTableResultProcessor

getResultsKey() - Method in class org.intermine.webservice.server.branding.BrandingService

getResultsKey() - Method in class org.intermine.webservice.server.core.JSONService

getResultsKey() - Method in class org.intermine.webservice.server.data.DataService

getResultsKey() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService

getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobResultsService

getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobStatusService

getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareCreationService

getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService

getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService

getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService

getResultsKey() - Method in class org.intermine.webservice.server.query.QueryStoreService

getResultsKey() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService

getResultsKey() - Method in class org.intermine.webservice.server.SchemaListService

getResultsKey() - Method in class org.intermine.webservice.server.SessionService

getResultsKey() - Method in class org.intermine.webservice.server.SummaryService

getResultsKey() - Method in class org.intermine.webservice.server.template.SingleTemplateService

getResultsKey() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService

getResultsKey() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService

getResultsKey() - Method in class org.intermine.webservice.server.user.ReadPreferencesService

getResultsKey() - Method in class org.intermine.webservice.server.user.TokenService

getResultsKey() - Method in class org.intermine.webservice.server.user.TokensService

getResultsKey() - Method in class org.intermine.webservice.server.user.WhoAmIService

getResultsKey() - Method in class org.intermine.webservice.server.VersionService

getResultsSize(String) - Static method in class org.intermine.dwr.AjaxServices

Return the number of rows of results from the query with the given query id.

getResultsTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods

Given a table identifier, return the cached PagedTable.

getResultsTablesLib() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getResultsWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess

Returns the (possibly uninitialised) results object used internally by this object, for use by subclass constructors.

getResultTable() - Method in interface org.intermine.web.logic.widget.DataSetLdr

Return the result table that represents the data from this widget.

getResultTable() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader

getReturnToString() - Method in class org.intermine.web.struts.LoginForm

Return the returnToString set by setReturnToURL().

getReverseAliases() - Method in class org.intermine.objectstore.query.Query

Returns the map of String aliases to QuerySelectables and FromElements

getRight() - Method in class org.intermine.objectstore.query.OverlapConstraint

Returns the right OverlapRange.

getRight() - Method in class org.intermine.sql.query.Constraint

Returns the right argument of the constraint.

getRight() - Method in class org.intermine.sql.query.InListConstraint

Returns the right Set of Constants.

getRight() - Method in class org.intermine.sql.writebatch.Row

Returns right.

getRightArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Get the right argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.

getRightColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Returns the right column name.

getRightField() - Method in class org.intermine.api.query.range.ConstraintOptions

Defaults to "end".

getRightOp() - Method in class org.intermine.api.query.range.ConstraintOptions

getRootClass() - Method in class org.intermine.pathquery.PathQuery

Returns the root path for this query, if the query verifies correctly.

getRootCVTerms() - Method in class org.intermine.bio.chado.ChadoCV

Return a Set of the root CVTerms in this CV - ie. those with no parents.

getRootElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getRootElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getRootElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter

getRootNode() - Method in class org.intermine.pathquery.LogicExpression

Get the root node.

getRootUrl() - Method in class org.intermine.webservice.client.core.Service

Returns service's root URL.

getRowElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

getRowElement() - Method in class org.intermine.webservice.server.output.XMLFormatter

getRowElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter

getRowFormatter() - Method in class org.intermine.webservice.server.output.FlatFileFormatter

Get the row formatter

getRowIterator(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService

getRowIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Returns a specific set of the results of a specified PathQuery as an iterator.

getRowIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Returns an iterator over a subset of rows for the template when run with the given parameters.

getRowIterator(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService

getRowListIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get an iterator over the results of a query.

getRowListIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get an iterator over the results of a query.

getRowListIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Get an iterator over the results of a query.

getRowListIterator(String) - Method in class org.intermine.webservice.client.services.QueryService

Get an iterator over the results of a query.

getRowListIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Get an iterator over the results of a query.

getRowListIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Get an iterator over the results of a query.

getRowMapIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get an iterator over the results of a query.

getRowMapIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get an iterator over the results of a query.

getRowMapIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Get an iterator over the results of a query.

getRowMapIterator(String) - Method in class org.intermine.webservice.client.services.QueryService

Get an iterator over the results of a query.

getRowMapIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Get an iterator over the results of a query.

getRowMapIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Get an iterator over the results of a query.

getRows(PathQuery) - Method in class org.intermine.api.mines.LocalMine

getRows(String) - Method in class org.intermine.api.mines.LocalMine

getRows(PathQuery) - Method in interface org.intermine.api.mines.Mine

Run a path query and get back all the results.

getRows(String) - Method in interface org.intermine.api.mines.Mine

Run a path query and get back all the results.

getRows(PathQuery) - Method in class org.intermine.api.mines.RemoteMine

getRows(String) - Method in class org.intermine.api.mines.RemoteMine

getRows() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns the estimated number of rows in the results.

getRows() - Method in class org.intermine.sql.query.ExplainResult

Returns the number of rows estimated by the database for this query.

getRows() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the currently visible rows of the table as a List of Lists of ResultElement objects.

getRows() - Method in class org.intermine.web.tags.table.TableTag

getRows(Request, List<String>) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Performs the actual remote request and fetches the results.

getRows(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService

getRows(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService

getRows() - Method in class org.intermine.webservice.server.core.SubTable

getRowsAsLists() - Method in class org.intermine.webservice.client.results.RowResultSet

Get the data for this result set in a parsed form.

getRowsAsLists(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get results for a query as rows of objects.

getRowsAsLists(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get results for a query as rows of objects.

getRowsAsLists(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Get results for a query as rows of objects.

getRowsAsLists(String) - Method in class org.intermine.webservice.client.services.QueryService

Get results for a query as rows of objects.

getRowsAsLists(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Get results for a query as rows of objects.

getRowsAsLists(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Get results for a query as rows of objects.

getRowsAsMaps() - Method in class org.intermine.webservice.client.results.RowResultSet

Get the data for this result set in a parsed form.

getRowsAsMaps(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get results for a query as rows of objects.

getRowsAsMaps(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService

Get results for a query as rows of objects.

getRowsAsMaps(String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Get results for a query as rows of objects.

getRowsAsMaps(String) - Method in class org.intermine.webservice.client.services.QueryService

Get results for a query as rows of objects.

getRowsAsMaps(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService

Get results for a query as rows of objects.

getRowsAsMaps(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService

Get results for a query as rows of objects.

getRowsFromBatch(int, int, int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Gets a range of rows from within a batch

getRowspan() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

Returns the rowspan.

getRowSpan() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Used from JSP in rowspan attr of

getRowsToDelete() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Returns the Set of rows to delete.

getRowsToInsert() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Returns the Set of rows to insert.

getRunningQueryController(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get the QueryMonitor object corresponding to a running query id (qid).

getSampleQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

getSampleSize() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

The sample size, n.

getSampleSize() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getSavedBag(String, String) - Method in class org.intermine.api.bag.SharedBagManager

Perform a query to retrieve a bag's backing SavedBag

getSavedBagId() - Method in class org.intermine.api.profile.StorableBag

getSavedBags() - Method in class org.intermine.api.profile.Profile

Get the value of savedBags

getSavedBagsByStatus() - Method in class org.intermine.api.profile.Profile

Get the saved bags in a map of "status key" => map of lists

getSavedBagStatus() - Method in class org.intermine.dwr.AjaxServices

This method gets the latest bags from the session (SessionMethods) and returns them in JSON

getSavedQueries() - Method in class org.intermine.api.profile.Profile

Get the value of savedQueries

getSavedTemplateQuery() - Method in class org.intermine.api.template.ApiTemplate

Gets the saved template query object.

getSavedTemplates() - Method in class org.intermine.api.profile.Profile

Get the users saved templates

getSchema() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Returns the DatabaseSchema used by this ObjectStore.

getSchemaLocation(HttpServletRequest) - Static method in class org.intermine.webservice.server.query.AbstractQueryService

getScope() - Method in class org.intermine.web.struts.TemplateForm

Get the template scope.

getScore() - Method in class org.intermine.api.lucene.KeywordSearchHit

score

getScore() - Method in class org.intermine.bio.io.bed.BEDRecord

getScore() - Method in class org.intermine.bio.io.gaf.GAFRecord

getScore() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the score field of this record.

getScore() - Method in class org.intermine.web.search.KeywordSearchResult

return score

getSearchHits(BrowseHit[], Map<Integer, InterMineObject>) - Static method in class org.intermine.api.lucene.KeywordSearch

getSearchIndex(String) - Method in class org.intermine.api.search.SearchRepository

Retrieve a search index for a given type of web searchable objects.

getSearchItems() - Method in class org.intermine.api.search.SearchRepository

Returns an unmodifiable view of the the search items observed by this repository.

getSearchRepository() - Method in class org.intermine.api.profile.Profile

Get the SearchRepository for this Profile.

getSearchTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices

getSearchTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getSecondFieldName() - Method in class org.intermine.objectstore.query.QueryField

Returns the name of the second field.

getSecondLastClassDescriptor() - Method in class org.intermine.pathquery.Path

Returns the second to last ClassDescriptor in the path.

getSection(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression

Take a Collection of String variable names, and return the part of the Logic Expression that contains those variables.

getSectionTitle() - Method in class org.intermine.web.logic.config.FieldConfig

Get the section title (if sectionOnRight == true).

getSegmentedFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return a list of types where one logical feature is represented as multiple rows in the feature table.

getSelect() - Method in class org.intermine.objectstore.query.Query

Gets the SELECT list

getSelect() - Method in interface org.intermine.objectstore.query.Queryable

Returns the SELECT list.

getSelect() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the SELECT list.

getSelect() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the SELECT list.

getSelect() - Method in class org.intermine.sql.query.Query

Gets the list of select fields for this query.

getSelected() - Method in class org.intermine.web.struts.ModifyTemplateForm

Gets the selected templates

getSelected() - Method in class org.intermine.web.struts.WidgetForm

getSelectedAsString() - Method in class org.intermine.web.struts.WidgetForm

returns the value of the checkboxes checked by the user on the form.

getSelectedBags() - Method in class org.intermine.web.struts.ModifyBagForm

Gets the selected bags

getSelectedClass() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getSelectedConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint

Returns the constraint type selected.

getSelectedElements() - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Get a String array of selected bag elements

getSelectedExtraAttribute() - Method in class org.intermine.web.struts.WidgetForm

getSelectedExtraValue() - Method in class org.intermine.web.logic.query.DisplayConstraint

If editing an existing LOOKUP constraint return the value selected for the extra constraint field.

getSelectedObjects() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Gets the ids of the selected objects

getSelectedObjects() - Method in class org.intermine.web.struts.SaveBagForm

Gets the selected objects

getSelectedOp() - Method in class org.intermine.web.logic.query.DisplayConstraint

If the bag is selected, return the value setted with the method setSelectedBagOp If editing an existing constraint return the operation used.

getSelectedQueries() - Method in class org.intermine.web.struts.ModifyQueryForm

Gets the selected queries

getSelectedValue() - Method in class org.intermine.web.logic.query.DisplayConstraint

If editing an existing constraint, return the selected value.

getSelectionIds() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getSeqClsName() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return the sequence class name that was passed to the constructor.

getSeqIdentifier(String) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler

Return the identifier of this sequence, default implementation returns the id passed to it.

getSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the sequence Item set by setSequence()

getSequence() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getSequence(Set<Object>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Return the sequence number representing the state of the ObjectStore.

getSequence(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Returns an object representing the current state of the database, for fail-fast concurrency control.

getSequence(Set<Object>) - Method in interface org.intermine.objectstore.ObjectStore

Return the sequence number representing the state of the ObjectStore.

getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Returns an object representing the current state of the database, for fail-fast concurrency control.

getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Return the sequence number representing the state of the ObjectStore.

getSequence() - Method in class org.intermine.objectstore.query.Results

Returns the sequence that this Results object was created with

getSequence() - Method in class org.intermine.objectstore.query.ResultsBatches

Returns the sequence that this ResultsBatches object was created with

getSequenceID() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the sequenceID field of this record.

getSequenceOntology() - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory

getSequenceOntology(File, File) - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory

Given an OBO file, create a Sequence Ontology object

getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDBConverter

getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioFileConverter

getSerial() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Gets an ID number which is unique in the database.

getSerial() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets an ID number which is unique in the database.

getSerial() - Method in interface org.intermine.objectstore.ObjectStore

Gets an ID number which is unique in the database.

getSerial() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Gets an ID number which is unique in the database.

getSerial() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Gets an ID number which is unique in the database.

getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets an ID number which is unique in the database, given a Connection.

getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Overrides, in order to store recentSequences.

getSeriesLabels() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getSeriesPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getSeriesValues() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getService(String, String) - Method in class org.intermine.webservice.client.core.ServiceFactory

Creates a new service for general use.

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.RestfulServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.WebServiceServlet

Implement this to route requests.

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.AvailableListsServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListRenameServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListShareServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListSharingInvitationServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.query.QueryUploadServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.search.QuickSearchServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.result.TemplateResultServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateToListServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateUploadServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.NewUserServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.PermaTokensServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.WhoAmIServlet

getServiceBaseURL() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

getServices() - Method in class org.intermine.webservice.server.ServiceListingHandler

getServiceUrl() - Method in interface org.intermine.webservice.client.core.Request

Returns service URL.

getServiceUrl() - Method in class org.intermine.webservice.client.core.RequestImpl

Returns service URL.

getSession() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Get the session

getSession() - Method in class org.intermine.webservice.server.core.SessionlessRequest

getSession(boolean) - Method in class org.intermine.webservice.server.core.SessionlessRequest

getSessionIdentifier() - Method in class org.intermine.api.tracker.track.TrackAbstract

Return the session id

getSharedBags(Profile) - Method in class org.intermine.api.bag.BagManager

Fetch the shared bags for the given profile.

getSharedBags(Profile) - Method in class org.intermine.api.bag.SharedBagManager

Return a map containing the bags that the user in input has access because shared by someone else

getSharedBags() - Method in class org.intermine.api.profile.Profile

Return the shared bags for the profile.

getSharedBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager

Fetch bags shared by another user that contain the given id.

getShortName() - Method in class org.intermine.bio.util.OrganismData

Get the short of this organism, eg.

getShowIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Used from JSP

getShowImmediately() - Method in class org.intermine.web.displayer.ReportDisplayer

getShowImmediately() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Should we display this 'splayer immediately, wo/ waiting for the AJAX call?

getShowInHeader() - Method in class org.intermine.web.logic.config.InlineListConfig

getShowInInlineCollection() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the showInInlineCollection flag

getShowInListAnalysisPreviewTable() - Method in class org.intermine.web.logic.config.FieldConfig

getShowInQB() - Method in class org.intermine.web.logic.config.FieldConfig

getShowInResults() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the showInResults flag

getShowInSummary() - Method in class org.intermine.web.logic.config.FieldConfig

Return the value of the showInSummary flag

getShowLinksToObjects() - Method in class org.intermine.web.logic.config.InlineListConfig

getShowLinksToObjects() - Method in class org.intermine.web.logic.results.InlineList

getShowOnLeft() - Method in class org.intermine.web.logic.config.Displayer

getSimpleClass(Class<? extends FastPathObject>) - Static method in class org.intermine.util.DynamicUtil

Returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one.

getSimpleClass(FastPathObject) - Static method in class org.intermine.util.DynamicUtil

For the given object returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one class.

getSimpleClassName(Class<?>) - Static method in class org.intermine.util.DynamicUtil

Returns the simple class name for the given class or throws an exception if there are more than one.

getSimpleClassName(FastPathObject) - Static method in class org.intermine.util.DynamicUtil

Returns the simple class name for the given object or throws an exception if there are more than one.

getSimplePathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget

Returns the pathquery based on the classkey.

getSingleUseKey() - Method in class org.intermine.api.profile.Profile

Return a single use API key for this profile

getSingleUseKey() - Static method in class org.intermine.dwr.AjaxServices

Return the single use API key for the current profile

getSize() - Method in class org.intermine.api.profile.InterMineBag

getSize() - Method in class org.intermine.api.profile.InvalidBag

getSize() - Method in class org.intermine.api.profile.StorableBag

Returns the size of the bag.

getSize() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch

Returns the current amount of data, in bytes, held in this object.

getSize() - Method in interface org.intermine.sql.writebatch.Table

Returns the current amount of data, in bytes, held in this object.

getSize() - Method in class org.intermine.sql.writebatch.TableBatch

Returns the current amount of data, in bytes, held in this object.

getSize() - Method in class org.intermine.web.logic.results.DisplayField

Get the size of this collection

getSize() - Method in class org.intermine.web.logic.results.InlineList

getSize() - Method in class org.intermine.web.logic.widget.PopulationInfo

getSize() - Method in class org.intermine.webservice.client.lists.ItemList

getSize() - Method in class org.intermine.webservice.client.results.Page

Get the maximum size of this page.

getSize() - Method in class org.intermine.webservice.server.core.Page

getSizeFields() - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getSizeFields

getSizeValues() - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getSizeValues

getSizeValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getSizeValuesForField

getSkeleton() - Method in class org.intermine.dataloader.Source

Getter for skeleton.

getSkeletonSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter

Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.

getSkeletonSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.

getSome(String...) - Method in class org.intermine.web.security.KeyStorePublicKeySource

getSome(String...) - Method in interface org.intermine.web.security.PublicKeySource

Get multiple keys given a set of names.

getSoTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook

Get and store a SO term based on intermine item's class or featureType (if provided).

getSource() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the source field of this record.

getSource(Integer, String) - Method in class org.intermine.dataloader.DataTracker

Retrieve the Source for a specified field of an Object stored in the database.

getSource(String) - Method in class org.intermine.dataloader.ObjectDescription

Gets the source associated with the given fieldname.

getSourcePrimaryKeys(Source, Model) - Static method in class org.intermine.dataloader.DataLoaderHelper

Fetch all primary keys for the given source.

getSpecies() - Method in class org.intermine.bio.util.OrganismData

Get the species of this organism.

getSQLString() - Method in class org.intermine.sql.precompute.PrecomputedTable

Get a "CREATE TABLE" SQL statement for this PrecomputedTable.

getSQLString() - Method in class org.intermine.sql.query.AbstractConstraint

Returns a String representation of this AbstractConstraint object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.AbstractTable

Returns a String representation of this AbstractTable object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.AbstractValue

Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.Constant

Returns a String representation of this Constant object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.Constraint

Returns a String representation of this Constraint object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.ConstraintSet

Returns a String representation of this ConstraintSet object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.Field

Returns a String representation of this Field object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.Function

Returns a String representation of this Function object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.InListConstraint

Returns a String representation of this InListConstraint object, suitable for forming part of an SQL Query.

getSQLString() - Method in class org.intermine.sql.query.NotConstraint

Returns a String representation of this Constraint object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.OrderDescending

Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.Query

Convert this Query into a SQL String query.

getSQLString() - Method in class org.intermine.sql.query.SelectValue

Returns a String representation of this Field object, suitable for forming part of an SQL SELECT list.

getSQLString() - Method in interface org.intermine.sql.query.SQLStringable

Returns a String representation of this object, suitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.SubQuery

Returns a String representation of this SubQuery object, auitable for forming part of an SQL query.

getSQLString() - Method in class org.intermine.sql.query.SubQueryConstraint

Returns a String representation of this SubQueryConstraint object, suitable for forming part of an SQL Query.

getSQLString() - Method in class org.intermine.sql.query.Table

Returns a String representation of this Table object, suitable for forming part of an SQL query.

getSQLStringForPrecomputedTable(String) - Method in class org.intermine.sql.query.Query

Convert this Query into a SQL String query, without regard to the other members of the the UNION, with an extra field in the SELECT list.

getSQLStringNoUnion() - Method in class org.intermine.sql.query.Query

Convert this Query into a SQL String query, without regard to the other members of the UNION.

getSrc() - Method in class org.intermine.web.logic.config.Displayer

Get the source of this displayer

getStandardDeviation() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary

getStandardIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask

Add indexes for primary keys, indirection tables and 1-N relations to the relevant tables for a given ClassDescriptor

getStar(Model, String) - Static method in class org.intermine.webservice.client.util.PQUtil

Get a list of all the path-strings for the attributes of a given class.

getStart() - Method in interface org.intermine.api.query.range.Range

getStart() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the start field of this record.

getStart() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Get start value

getStart() - Method in class org.intermine.objectstore.query.OverlapRange

Returns the left parameter.

getStart() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns the estimated amount of time taken to produce the first row of the results.

getStart() - Method in class org.intermine.sql.query.ExplainResult

Returns the number of page requests before the first row is returned, estimated by the database for this query.

getStart() - Method in class org.intermine.webservice.client.results.Page

Get the start index of this page.

getStart() - Method in class org.intermine.webservice.server.core.Page

Get the index of the first row that is requested.

getStart() - Method in class org.intermine.webservice.server.WebServiceInput

Returns index of first returned result

getStartClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getStartClassDescriptor() - Method in class org.intermine.pathquery.Path

Return the ClassDescriptor of the first element in the path.

getStartClassDisplay() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getStartedAt() - Method in interface org.intermine.api.idresolution.Job

getStartedAt() - Method in class org.intermine.api.idresolution.ResolutionJob

getStartedAt() - Method in class org.intermine.api.idresolution.UpgradeJob

getStartingPoints() - Method in class org.intermine.web.logic.aspects.Aspect

Get a List of starting point class names.

getStartRow() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Get the index of the first row of this page

getState() - Method in class org.intermine.api.profile.InterMineBag

Return the bag state: current, not current, to upgrade

getState() - Method in class org.intermine.api.profile.InvalidBag

getState() - Method in class org.intermine.api.profile.StorableBag

Return a string representing the state of this bag (eg.

getState(String) - Method in class org.intermine.web.logic.results.WebState

getStatementCreatingTable() - Method in class org.intermine.api.tracker.AbstractTracker

Generate the sql statement to create the table used by the tracker

getStatementCreatingTable() - Method in class org.intermine.api.tracker.KeySearchTracker

getStatementCreatingTable() - Method in class org.intermine.api.tracker.ListTracker

Generate the sql statement to create the table used by the tracker

getStatementCreatingTable() - Method in class org.intermine.api.tracker.LoginTracker

Generate the sql statement to create the table used by the tracker

getStatementCreatingTable() - Method in class org.intermine.api.tracker.QueryTracker

Generate the sql statement to create the table used by the tracker

getStatementCreatingTable() - Method in class org.intermine.api.tracker.TemplateTracker

Generate the sql statement to create the table used by the tracker

getStates() - Method in class org.intermine.web.logic.results.WebState

getStaticPage(String, String) - Static method in class org.intermine.web.logic.WebUtil

Return the contents of the page given by prefixURLString + '/' + path as a String.

getStatus() - Method in interface org.intermine.api.idresolution.Job

getStatus() - Method in class org.intermine.api.idresolution.ResolutionJob

getStatus() - Method in class org.intermine.api.idresolution.UpgradeJob

getStatus() - Method in class org.intermine.objectstore.query.ResultsInfo

Returns an integer describing the type of estimate getRows() returns.

getStatus() - Method in class org.intermine.webservice.client.lists.ItemList

Any status other than CURRENT indicated this list needs manual attention in the webapp.

getStocksResultSet(Connection) - Method in class org.intermine.bio.dataconversion.StockProcessor

Return the interesting rows from the features table.

getStrain(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Get strain taxons.

getStrain() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

getStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

getStrain(String) - Method in class org.intermine.bio.util.OrganismRepository

Get strains for given taxon ID

getStrains() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

used for testing

getStrand() - Method in class org.intermine.bio.io.bed.BEDRecord

getStrand() - Method in class org.intermine.bio.io.gaf.GAFRecord

getStrand() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the strand field of this record.

getStrand() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Get strand value

getString(String) - Static method in class org.intermine.api.query.codegen.JSStrings

getString(String, Object...) - Static method in class org.intermine.api.query.codegen.JSStrings

getString(String) - Method in class org.intermine.webservice.client.results.Item

Get a property known to be a string.

getStringResponse(Request, Integer) - Method in class org.intermine.webservice.client.core.Service

Performs the request and returns the result as a string.

getStringResponse(Request) - Method in class org.intermine.webservice.client.core.Service

Performs the request and returns the result as a string.

getStructure() - Method in class org.intermine.web.logic.query.MetadataNode

Returns the structure of the tree.

getStructure() - Method in class org.intermine.web.logic.TreeNode

Returns the structure of the tree.

getStyle() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Returns element style.

getStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Returns css style class of element.

getSubclass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns the subclass if it exists.

getSubclass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Returns the subclass if it exists.

getSubclass() - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Returns the name of the subclass on this path, if there is one.

getSubClassConstraintPaths() - Method in class org.intermine.pathquery.Path

Returns a Map from simplified path string (with dots instead of colons, and no constraints) to constraint class name.

getSubclasses() - Method in class org.intermine.pathquery.PathQuery

Returns the subclass Map for this query, if the query verifies correctly.

getSubclassValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Gets the value of subclassValue

getSubject() - Method in class org.intermine.web.struts.ContactForm

getSubmissionOrganism(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the row needed for the organism.

getSubmissions(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Return the rows needed for the submission table.

getSubSequence() - Method in class org.intermine.objectstore.query.ClobAccess

Returns true if this object is a subsequence of a main Clob.

getSubtab(String) - Method in class org.intermine.web.logic.results.WebState

getSubtabs() - Method in class org.intermine.web.logic.results.WebState

map of tab --> subtab

getSubTitle() - Method in class org.intermine.web.logic.aspects.Aspect

Get the subtitle

getSubTitles() - Method in class org.intermine.web.logic.config.Type

getSubtractLists() - Method in class org.intermine.webservice.server.lists.ListInput

getSubType() - Method in class org.intermine.webservice.client.core.ContentType

getSuffix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart

A suffix that may be an HTML tag to appear after this part in the title.

getSummary(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Returns a StringBuffer containing summary information.

getSummary(Source) - Method in class org.intermine.dataloader.HintingFetcher

Returns a StringBuffer containing summary information.

getSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService

Get a summary for the values in column of a query.

getSummary(PathQuery, String, Page) - Method in class org.intermine.webservice.client.services.QueryService

Get a summary for the values in column of a query.

getSuperuser() - Method in class org.intermine.api.profile.Profile

Alias of isSuperUser() for jsp purposes.

getSuperuser() - Method in class org.intermine.api.profile.ProfileManager

Return the super user name set in the properties file

getSuperuserProfile() - Method in class org.intermine.api.profile.ProfileManager

Return the superuser profile set in the properties file

getSuperuserProfile(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Return the super user

getSuperUsers() - Method in class org.intermine.api.profile.ProfileManager

Return a list of users with 'superuser' role

getSuperUsers() - Method in class org.intermine.web.struts.ModifySuperUserForm

Get the super users

getSuperUsersProfile() - Method in class org.intermine.api.profile.ProfileManager

Return a list of profile with 'superuser' role

getSwitchable() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the value on, off, locked depending on the constraint SwitchOffAbility .

getSwitchable() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Get the switchoffAbility for a constraint.

getSwitchable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the switchable value (on, off, locked).

getSwitchOff(String) - Method in class org.intermine.web.struts.TemplateForm

Get the SwitchOff ability.

getSwitchOffAbility(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Gets the sbitch-off-ability of a constraint.

getSwitchOffAbility() - Method in class org.intermine.template.TemplateValue

Returns the SwitchOffAbility.

getSynonym(Item, String) - Method in class org.intermine.bio.dataconversion.GFF3Converter

Create and add a synonym Item from the given information.

getSynonymResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the interesting rows from the synonym table.

getSynonyms() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

getSynonyms(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

For a particular primary identifier fetch a set of synonyms or return null if id is not a primary identifier for the taxonId given.

getSynonyms(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

For a particular primary identifier fetch a set of synonyms or return null if id is not a primary identifier for the taxonId given.

getSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry

used to assign sequences

getSynonyms() - Method in class org.intermine.bio.ontology.OboTerm

Get a set of synonyms (Strings) for this term.

getTable() - Method in class org.intermine.sql.query.Field

Returns the table of this field.

getTable() - Method in class org.intermine.web.logic.results.DisplayField

Get the inline results table for this collection

getTable() - Method in class org.intermine.web.struts.TableExportForm

Get the table identifier to look up the PagedTable in the servlet context

getTableCount() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

Returns the number of tables in this query.

getTableDefinition() - Static method in class org.intermine.api.bag.SharingInvite

getTableDefinition(Database, ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil

getTableDisplayer() - Method in class org.intermine.web.logic.config.Type

Get the table Displayer

getTableExportConfigs() - Method in class org.intermine.web.logic.config.WebConfig

Return a Map of TableExportConfig.id to TableExportConfig objects.

getTableFieldConfigs() - Method in class org.intermine.web.logic.results.InlineResultsTable

getTableFields(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns a Fields object of FieldDescriptors in the given table-mastering ClassDescriptor.

getTableid() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getTableInfo(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Produces metadata for a given table, caching it to save time.

getTableMaster(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns the name of the table in which to store a row for the given ClassDescriptor.

getTableName() - Method in class org.intermine.api.tracker.track.KeySearchTrack

getTableName() - Method in class org.intermine.api.tracker.track.ListTrack

Return the table name where the track has to be saved

getTableName() - Method in class org.intermine.api.tracker.track.LoginTrack

Return the table name where the track has to be saved

getTableName() - Method in class org.intermine.api.tracker.track.QueryTrack

getTableName() - Method in class org.intermine.api.tracker.track.TemplateTrack

Return the table name where the track has to be saved

getTableName() - Method in interface org.intermine.api.tracker.track.Track

Return the table name where the track has to be saved

getTableName(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil

Creates a table name for a class descriptor

getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

Returns the approximate number of rows in a table.

getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Returns the approximate number of rows in a table.

getTabLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

Returns link which gives results as lines, where values are tab separated.

getTagById(int) - Method in class org.intermine.api.profile.TagManager

Get Tag by object id.

getTagManager() - Method in interface org.intermine.api.API

getTagManager() - Method in class org.intermine.api.InterMineAPI

getTagManager() - Method in class org.intermine.api.profile.ProfileManager

Return the TagManager for adding, removing and fetching Tags assigned to templates, bags and classes.

getTagManager() - Method in class org.intermine.api.profile.TagManagerFactory

getTagName() - Method in class org.intermine.api.search.TaggingEvent

getTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager

Deprecated.

There are typed methods that are more suitable. Use them instead.

getTags(ApiTemplate, Profile) - Method in class org.intermine.api.template.TemplateManager

For a (public or private) template, return all the tags.

getTags(String) - Static method in class org.intermine.dwr.AjaxServices

Returns all tags of specified tag type together with prefixes of these tags.

getTags() - Method in class org.intermine.webservice.client.lists.ItemList

Modifying the returned set will not change the underlying tags collection.

getTags(ItemList) - Method in class org.intermine.webservice.client.services.ListService

Get the most current tag set for a list.

getTags() - Method in class org.intermine.webservice.server.lists.ListInput

getTagsByName(String, Profile, String) - Method in class org.intermine.api.profile.TagManager

Return all the tags with the given tag name, optionally filtered by tag-type.

getTagsByType(String) - Method in class org.intermine.api.profile.TagManager

Return all tags of given type.

getTagsForBag(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager

Get a list of tags for a given bag.

getTagString() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo

Get the tags joined in the manner required for the list service.

getTagType() - Method in class org.intermine.api.profile.StorableBag

getTagType() - Method in interface org.intermine.api.profile.Taggable

Poly-Morphic Constant.

getTagType() - Method in class org.intermine.api.template.ApiTemplate

getTagValues() - Method in class org.intermine.bio.ontology.OboTerm

Gets the tagValues.

getTarget() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the first value of the Target field from the attributes of this record.

getTargetModel() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the Model that was passed to the constructor.

getTargets() - Method in class org.intermine.webservice.client.widget.Widget

getTargetType() - Method in class org.intermine.api.bag.AdditionalConverter

getTaxonId() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

getTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

getTaxonId() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getTaxonId() - Method in class org.intermine.bio.util.OrganismData

Get the taxonId of this organism.

getTaxons() - Method in class org.intermine.bio.dataconversion.IdResolver

Return a set of taxon id.

getTaxonsAndClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver

Get a set of keys (taxon id + class name) resolver holds

getTemplate(String) - Method in class org.intermine.api.profile.Profile

get a template

getTemplate(Profile, String, String) - Method in class org.intermine.api.template.TemplateManager

Fetch a template with the scope provided, possible values are defined in Scope class.

getTemplate(String) - Method in class org.intermine.webservice.client.services.TemplateService

Get the template with the given name, if accessible.

getTemplateButton() - Method in class org.intermine.web.struts.ModifyTemplateForm

getTemplateLabel() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the template label.

getTemplateManager() - Method in interface org.intermine.api.API

getTemplateManager() - Method in class org.intermine.api.InterMineAPI

getTemplateManager() - Static method in class org.intermine.api.query.PathQueryAPI

Returns the TemplateManager for access to global and user template queries.

getTemplateName() - Method in class org.intermine.api.tracker.track.TemplateTrack

Return the template name

getTemplateNames() - Method in class org.intermine.webservice.client.services.TemplateService

Get the names of the templates to which the current user has access.

getTemplates() - Method in class org.intermine.web.search.KeywordSearchResult

templates associated with this class

getTemplates() - Method in class org.intermine.webservice.client.services.TemplateService

Get the templates to which the current user has access.

getTemplateService() - Method in class org.intermine.webservice.client.core.ServiceFactory

Return a new QueryService for getting query results from.

getTemplatesForType(String) - Method in class org.intermine.webservice.client.services.TemplateService

Get all the templates with constraints which constrain paths of a certain type.

getTemplateSummariser() - Method in interface org.intermine.api.API

getTemplateSummariser() - Method in class org.intermine.api.InterMineAPI

getTemplateTracker() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the tracker template

getTemplateTracksPercentage(String) - Method in class org.intermine.dwr.TrackAjaxServices

getTemplateTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices

getTemporaryListName() - Method in class org.intermine.webservice.server.lists.ListInput

getTermIdNameMap(Reader) - Method in class org.intermine.bio.ontology.OboParser

Parse an OBO file to produce a map from ontology term id to name.

getTestCount() - Method in interface org.intermine.web.logic.widget.EnrichmentInput

The test count represents the number of tests that will be performed.

getTestCount() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr

getText() - Method in class org.intermine.web.logic.config.HeaderConfigLink

getText() - Method in class org.intermine.web.logic.TreeNode

Get the text that was passed to the constructor

getText() - Method in class org.intermine.web.struts.BuildBagForm

Get the text string

getTextToFind() - Method in class org.intermine.web.struts.FindInListForm

getTgtLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the tgtLocation Item set by setTgtLocation()

getTgtModel() - Method in class org.intermine.bio.dataconversion.GFF3Converter

Return the

getTgtOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Return the tgtOrganism Item set by setTgtOrganism()

getTgtSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Get the target Sequence Item set by setTgtSequence().

getThickEnd() - Method in class org.intermine.bio.io.bed.BEDRecord

getThickEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord

getThickStart() - Method in class org.intermine.bio.io.bed.BEDRecord

getThickStart() - Method in class org.intermine.bio.io.gaf.GAFRecord

getTickleCount() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Find out how many times tickle has been called.

getTileName() - Method in class org.intermine.web.logic.aspects.Aspect

Get the name of tile/page to embed in the centre of the data set homepage

getTime() - Method in class org.intermine.sql.query.DummyExplainResult

Returns an estimate of the time it will take to complete the query.

getTime() - Method in class org.intermine.sql.query.ExplainResult

Returns an estimate of the time it will take to complete the query.

getTimeLimit() - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Returns the time limit.

getTimestamp() - Method in class org.intermine.api.tracker.track.TrackAbstract

Return the timestamp of the event

getTitle() - Method in class org.intermine.api.bag.AdditionalConverter

getTitle() - Method in class org.intermine.api.profile.InterMineBag

The user-friendly title for this object.

getTitle() - Method in class org.intermine.api.profile.InvalidBag

getTitle() - Method in interface org.intermine.api.search.WebSearchable

The user-friendly title for this object.

getTitle() - Method in class org.intermine.pathquery.PathQuery

Gets the title for this query.

getTitle() - Method in class org.intermine.template.TemplateQuery

getTitle() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return the last class in the path and fieldname as the title for the constraint.

getTitle() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getTitle() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

Get the title

getTitle() - Method in class org.intermine.web.logic.widget.Widget

Get the widget title

getTitle() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

title of the widget

getTitle() - Method in class org.intermine.web.struts.TemplateSettingsForm

Return the title

getTitle() - Method in class org.intermine.webservice.client.widget.Widget

getTitleMain() - Method in class org.intermine.web.logic.results.ReportObject

Used by JSP

getTitles() - Method in class org.intermine.web.logic.config.HeaderConfigTitle

getTitleSub() - Method in class org.intermine.web.logic.results.ReportObject

Used by JSP

getToggledElements() - Static method in class org.intermine.dwr.AjaxServices

This method gets a map of ids of elements that were in the past (during session) toggled and returns them in JSON

getToggledElements() - Method in class org.intermine.web.logic.results.WebState

Gets map of ids of elements that were in the past (during session) toggled - if they are opened or closed.

getToken() - Method in class org.intermine.api.bag.SharingInvite

getToken() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

getToken() - Method in class org.intermine.web.struts.PasswordResetForm

Gets the value of token.

getToken() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService

getTokenUrl() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider

getTokenUrl() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider

getTokenUrl() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider

getTotalHits() - Method in class org.intermine.api.lucene.ResultsWithFacets

getTracker(String, Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.factory.TrackerFactory

Return the tracker instantiated with the reflection

getTracker(String) - Method in class org.intermine.api.tracker.TrackerDelegate

Return the tracker specified in input

getTrackerDelegate() - Method in interface org.intermine.api.API

getTrackerDelegate() - Method in class org.intermine.api.InterMineAPI

getTrackers() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the trackers saved in the TrackerManager

getTrackTableName() - Method in class org.intermine.api.tracker.AbstractTracker

Return the table's name associated to the tracker

getTrail() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

Get the trail URL parameter for this trail element.

getTransitiveOver() - Method in class org.intermine.bio.ontology.OboTypeDefinition

getTranslator() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Returns the Translator associated with the underlying ObjectStoreTranslatingImpl.

getTranslator() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Return the Translator that was passed to the constructor.

getType() - Method in class org.intermine.api.bag.BagQueryUpgrade

getType() - Method in class org.intermine.api.beans.ObjectDetails

getType() - Method in interface org.intermine.api.idresolution.Job

getType() - Method in interface org.intermine.api.idresolution.JobInput

getType() - Method in class org.intermine.api.idresolution.ResolutionJob

getType() - Method in class org.intermine.api.idresolution.UpgradeJob

getType() - Method in class org.intermine.api.lucene.KeywordSearchFacetData

type of facet

getType() - Method in class org.intermine.api.profile.InterMineBag

Get the type of this bag (a class from InterMine model)

getType() - Method in class org.intermine.api.profile.InvalidBag

getType() - Method in class org.intermine.api.profile.StorableBag

Get the unqualified name of class that the objects in this bag represent.

getType() - Method in class org.intermine.api.results.Column

Return the type of this Column

getType() - Method in interface org.intermine.api.results.ResultCell

getType() - Method in class org.intermine.api.results.ResultElement

Get the type

getType() - Method in class org.intermine.api.tracker.track.ListTrack

Return the class type of items contained into the list

getType() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref

getType() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return the type field of this record.

getType() - Method in class org.intermine.bio.ontology.OboTermSynonym

Get the synonym type.

getType(FieldDescriptor) - Method in class org.intermine.codegen.JavaModelOutput

Return the java type of a particular field.

getType() - Method in class org.intermine.dataloader.Source

getType() - Method in class org.intermine.objectstore.query.Clob

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.ObjectStoreBag

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.OrderDescending

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.PathExpressionField

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryCast

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryClass

Gets the Java class represented by this QueryClass

getType() - Method in class org.intermine.objectstore.query.QueryClassBag

Gets the Java class represented by this QueryClassBag.

getType() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryCollectionReference

Gets the Java class of this QueryReference.

getType() - Method in class org.intermine.objectstore.query.QueryExpression

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryField

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryForeignKey

Gets the Java class of this QueryReference.

getType() - Method in class org.intermine.objectstore.query.QueryFunction

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryObjectReference

Gets the Java class of this QueryReference.

getType() - Method in interface org.intermine.objectstore.query.QueryOrderable

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryReference

Gets the Java class of this QueryReference.

getType() - Method in interface org.intermine.objectstore.query.QuerySelectable

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.QueryValue

Get Java type represented by this item.

getType() - Method in class org.intermine.objectstore.query.WidthBucketFunction

Get Java type represented by this item.

getType() - Method in class org.intermine.pathquery.Node

Gets the value of type

getType(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint

A static method to get the type of this constraint if it is a sub-class constraint, or otherwise return null.

getType() - Method in class org.intermine.pathquery.PathConstraintSubclass

Returns the class that the constraint is constraining to.

getType() - Method in class org.intermine.web.logic.bag.WebJobInput

getType() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns the type of the value represented by this path, as a string.

getType() - Method in class org.intermine.web.logic.results.ReportObject

Get the unqualified class name for the report object.

getType() - Method in class org.intermine.web.logic.WebUtil.HeadResource

getType() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

getType() - Method in class org.intermine.web.search.KeywordSearchResult

returns the name of the class for this object (category)

getType() - Method in class org.intermine.web.struts.BuildBagForm

Get the bag type

getType() - Method in class org.intermine.web.struts.CSVExportForm

Return the export type: "tab", etc.

getType() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

Return whether or not this trail element refers to a table.

getType() - Method in class org.intermine.web.struts.TableExportForm

Return the export type: "tab", etc.

getType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Returns type of tag.

getType() - Method in class org.intermine.webservice.client.core.ContentType

getType() - Method in interface org.intermine.webservice.client.core.Request

getType() - Method in class org.intermine.webservice.client.core.RequestImpl

getType() - Method in class org.intermine.webservice.client.lists.ItemList

getType() - Method in class org.intermine.webservice.client.results.Item

Get the type of this object.

getType() - Method in class org.intermine.webservice.server.core.TableCell

getType() - Method in class org.intermine.webservice.server.lists.ListInput

getType() - Method in class org.intermine.webservice.server.lists.ListsServiceInput

getTypeClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getTypeClsString() - Method in class org.intermine.api.results.Column

Get the column type unqualified as a String

getTypeForColumn(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the class from the data model for the data displayed in indexed column.

getTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Get the comma separated unqualified class names for which this displayer should be displayed.

getTypes() - Method in class org.intermine.web.logic.config.WebConfig

Get a map from fully qualified class name to the Type config for that class

getUid() - Method in interface org.intermine.api.idresolution.Job

getUid() - Method in class org.intermine.api.idresolution.ResolutionJob

getUid() - Method in class org.intermine.api.idresolution.UpgradeJob

getUnencodedUrl() - Method in interface org.intermine.webservice.client.core.Request

getUnencodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl

getUnformatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue

Get the unformatted version that is just the field value.

getUnion() - Method in class org.intermine.sql.query.Query

Returns the List of queries in the UNION set of this query.

getUniprot() - Method in class org.intermine.bio.util.OrganismData

getUniprotAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry

getUniqueIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

eg. primaryIdentifier

getUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig

getUniqueInteger(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Return a unique integer from a SEQUENCE in the database.

getUniqueItemId(String) - Method in class org.intermine.dataconversion.DataConverter

List of unique identifiers and their refIds.

getUnmatchedIdentifiers() - Method in class org.intermine.webservice.client.lists.ItemList

Get the identifiers used in creating or appending to this list that could not be resolved to any objects.

getUnqualifiedClassName() - Method in class org.intermine.web.logic.config.Type

getUnresolved() - Method in class org.intermine.api.bag.BagQueryResult

Deprecated.

Use getUnresolvedIdentifiers

getUnresolvedIdentifiers() - Method in class org.intermine.api.bag.BagQueryResult

Get all the unresolved identifiers.

getUnusedListName() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo

Get a name for the list if none has been supplied.

getUpdatedPathQuery() - Method in class org.intermine.api.profile.PathQueryUpdate

Return a new pathquery updated to the new model

getUrl() - Method in class org.intermine.api.mines.LocalMine

getUrl() - Method in interface org.intermine.api.mines.Mine

getUrl() - Method in class org.intermine.api.mines.RemoteMine

getURL() - Method in class org.intermine.sql.Database

Gets the URL from this database

getUrl() - Method in class org.intermine.web.logic.aspects.AspectSource

Get the URL back to source website.

getUrl() - Method in class org.intermine.web.logic.config.HeaderConfigLink

getUrl() - Method in class org.intermine.web.logic.WebUtil.HeadResource

getUrl() - Method in class org.intermine.webservice.client.core.Service

Returns service URL Example: http://www.flymine.org/query/service/query/results

getUrlField() - Method in class org.intermine.api.bag.AdditionalConverter

getUseBagConstraint(String) - Method in class org.intermine.web.struts.TemplateForm

Get the value of useBagConstraint for given constraint key.

getUseJoin() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

getUser() - Method in class org.intermine.sql.Database

Gets the username for this Database

getUserAndGlobalTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager

Fetch all user and global templates in a single map for the given user.

getUserBag(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch a user bag by name.

getUserBags(Profile) - Method in class org.intermine.api.bag.BagManager

Fetch bags for the given profile.

getUserBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager

Fetch user bags that contain the given id.

getUserBagsWithTag(Profile, String) - Method in class org.intermine.api.bag.BagManager

Fetch bags from given protocol with a particular tag assigned to them.

getUserBagsWithTags(Profile, List<String>) - Method in class org.intermine.api.bag.BagManager

Give me profile bags matching a set of tags

getUserId() - Method in class org.intermine.api.profile.Profile

Get the value of userId

getUserLogin(Connection) - Method in class org.intermine.api.tracker.LoginTracker

Return the number of access for each user

getUserLogin() - Method in class org.intermine.api.tracker.TrackerDelegate

Return the number of access for each user

getUsername() - Method in class org.intermine.api.profile.Profile

Get the value of username

getUserName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

The name of the user logged in when this info was generated

getUserName() - Method in class org.intermine.api.tracker.track.TrackAbstract

Return the user name

getUsername() - Method in class org.intermine.api.util.AnonProfile

getUsername() - Method in class org.intermine.web.struts.CreateAccountForm

getUsername() - Method in class org.intermine.web.struts.LoginForm

Gets the value of username The user name is always returned in LOWER CASE.

getUsername() - Method in class org.intermine.web.struts.RequestPasswordForm

Gets the value of username

getUserName() - Method in class org.intermine.webservice.server.WebServiceInput

getUsernameForToken(String) - Method in class org.intermine.api.profile.ProfileManager

Returns the username associated with the given token, if the token is valid.

getUserOrGlobalTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager

Fetch a user or global template by name.

getUserProfile() - Method in class org.intermine.api.InterMineAPI

getUserProfile(String) - Method in class org.intermine.api.profile.ProfileManager

Perform a query to retrieve a user's backing UserProfile

getUserProfile(Integer) - Method in class org.intermine.api.profile.ProfileManager

Perform a query to retrieve a user's backing UserProfile

getUserProfileWriter() - Method in class org.intermine.api.profile.InterMineBag

getUserProfileWriter() - Method in class org.intermine.api.profile.InvalidBag

getUserProfileWriter() - Method in class org.intermine.api.profile.StorableBag

Get a reference to a connection to the database where user data is persisted.

getUsersSharingBag(String, String) - Method in class org.intermine.api.bag.BagManager

Return the users sharing the list given in input, not the owner

getUsersSharingBag(String) - Method in class org.intermine.dwr.AjaxServices

Return the list of users who have access to this bag because it has been shared with them.

getUsersWithAccessToBag(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager

Return the users this bag is shared with.

getUserTagNames(String, Profile) - Method in class org.intermine.api.profile.TagManager

Returns names of tags of specified user and tag type.

getUserTagNames(String, String) - Method in class org.intermine.api.profile.TagManager

Deprecated.

It is better to use the typed methods instead.

getUserTags(String) - Method in class org.intermine.api.profile.TagManager

Returns tags of specified user.

getUserTags(Profile) - Method in class org.intermine.api.profile.TagManager

Returns tags of specified user.

getUserTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager

Fetch a user template by name.

getUserToken() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

A token for the user.

getUserWithUniqueMapping(String, String) - Method in class org.intermine.api.profile.PreferencesManager

getUUID() - Method in class org.intermine.webservice.server.user.DeletionToken

getValidGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager

Return a map from template name to template query containing superuser templates that are tagged as public and are valid for the current data model.

getValidOps() - Method in class org.intermine.web.logic.query.DisplayConstraint

Given the path being constrained return the valid constraint operations.

getValidRangeTargets() - Static method in class org.intermine.api.query.MainHelper

getValue() - Method in class org.intermine.api.lucene.KeywordSearchFacet

selected value

getValue() - Method in class org.intermine.api.profile.BagValue

getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

Returns the value of the entry.

getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue

Returns the value of the entry.

getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowValue

Returns the value of the entry.

getValue() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig

getValue() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref

getValue() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject

Returns the value.

getValue() - Method in class org.intermine.objectstore.query.QueryCast

Returns the QueryEvaluable that is the actual value.

getValue() - Method in class org.intermine.objectstore.query.QueryValue

Returns the object that is the actual value.

getValue() - Method in class org.intermine.objectstore.query.UnknownTypeValue

Returns the value.

getValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint

A static method for accessing values without having to handle the subclasses manually.

getValue() - Method in class org.intermine.pathquery.PathConstraintAttribute

Returns the value that the constraint is constraining to.

getValue() - Method in class org.intermine.pathquery.PathConstraintLookup

Returns the lookup value for this constraint.

getValue() - Method in class org.intermine.sql.query.OrderDescending

Returns the value.

getValue() - Method in class org.intermine.sql.query.SelectValue

Gets the AbstractValue from this object.

getValue() - Method in class org.intermine.template.TemplateValue

Returns value.

getValue() - Method in class org.intermine.web.logic.config.InlineListObject

Fetch the column value, ie "Zerknullt" for Synonyms of a Gene

getValue() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Get a string representation of the constraint value to be displayed.

getValue() - Method in class org.intermine.web.logic.results.ReportObjectField

Get field value

getValue() - Method in class org.intermine.web.logic.template.ConstraintInput

Returns constraint value.

getValue() - Method in class org.intermine.webservice.client.template.TemplateParameter

Returns value.

getValue() - Method in class org.intermine.webservice.server.core.Pair

getValue() - Method in class org.intermine.xml.full.Attribute

Get the value of this field

getValueHasDisplayer() - Method in class org.intermine.web.logic.results.ReportObjectField

Does the field have a custom displayer defined for the value?

getValueMap() - Method in class org.intermine.sql.precompute.PrecomputedTable

Gets a Map from AbstractValue to SelectValue for the Query in this PrecomputedTable.

getValues(String) - Method in class org.intermine.dataloader.EquivalentObjectHints

Returns a Set of values that were in the database for a particular class and fieldname.

getValues(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint

Get the values for a constraint.

getValues() - Method in class org.intermine.pathquery.PathConstraintMultiValue

Returns the value collection that the constraint is constraining to.

getValues() - Method in class org.intermine.template.TemplateValue

getValues() - Method in class org.intermine.webservice.client.template.TemplateParameter

getValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getValuesForField

getValuesForField(String, int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass

getValuesForField

getValuesFromInput(TemplateQuery, TemplateResultInput) - Static method in class org.intermine.web.logic.template.Templates

Creates a map from input to be used later to populate the template.

getVariableNames() - Method in class org.intermine.pathquery.LogicExpression

Get the Set of variable names.

getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets the verboseQueryLog configuration option.

getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Gets the verboseQueryLog configuration option.

getVersion() - Method in class org.intermine.api.profile.ProfileManager

Returns the version number of the data format in the database for this ProfileManager.

getVersion() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns the database format version.

getVersion() - Method in class org.intermine.sql.Database

Get the version number of the database as a string.

getVersion() - Method in class org.intermine.webservice.client.core.Service

getView() - Method in class org.intermine.pathquery.PathQuery

Returns the current view list.

getView() - Method in class org.intermine.web.struts.TemplateForm

Get the selected alternative view name.

getViewPaths() - Method in class org.intermine.api.results.ExportResultsIterator

getViews() - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getVisibleColumnCount() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return the number of visible columns.

getVisibleIndexes() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Returns indexes of columns, that should be displayed.

getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator

Returns warnings occurred during parsing xml.

getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

Returns warning occurred during parsing xml.

getWebConfig() - Static method in class org.intermine.web.context.InterMineContext

getWebConfig(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods

getWebConfig(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

getWebConfig() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getWebProperties() - Static method in class org.intermine.web.context.InterMineContext

getWebProperties(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns the web properties.

getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods

Returns the web properties.

getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.struts.InterMineAction

Get the web proprties.

getWebResultsExecutor(Profile) - Method in interface org.intermine.api.API

getWebResultsExecutor(Profile) - Method in class org.intermine.api.InterMineAPI

getWebSearchableMap(String) - Method in class org.intermine.api.search.GlobalRepository

Get a map from name -> object for all the websearchables of the given type.

getWebSearchableMap(String) - Method in class org.intermine.api.search.SearchRepository

Get a map from name -> object for all the websearchables of the given type.

getWebSearchablesByType(String) - Method in class org.intermine.api.profile.Profile

Return a WebSearchable Map for the given type.

getWebState(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Get WebState object that is used for saving state of webapp GUI.

getWebTable() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

getWhere() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getWhere() - Method in class org.intermine.sql.query.Query

Gets the Set of constraints in the where clause of this query.

getWhereBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

getWhichInput() - Method in class org.intermine.web.struts.BuildBagForm

Get the method the user used to upload the bag.

getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig

getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

getWidget(String) - Method in class org.intermine.webservice.client.services.WidgetService

getWidgetid() - Method in class org.intermine.web.struts.WidgetForm

getWidgetId() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

Get the name or id of the widget

getWidgets() - Method in class org.intermine.web.logic.config.Type

getWidgets() - Method in class org.intermine.web.logic.config.WebConfig

getWidgets() - Method in class org.intermine.webservice.client.services.WidgetService

getWidgetService() - Method in class org.intermine.webservice.client.core.ServiceFactory

Return the WidgetService for retrieving widget information.

getWidgetTitle() - Method in class org.intermine.web.struts.WidgetForm

used on results page for description: "results for widget XYZ"

getWidgetTotal() - Method in interface org.intermine.web.logic.widget.DataSetLdr

This method is used to calculate the 'not analysed' total displayed on each widget

getWidgetTotal() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader

getWidgetTotal() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

getWidgetType() - Method in class org.intermine.webservice.client.widget.Widget

getWidgetType(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl

getWidth() - Method in class org.intermine.sql.query.ExplainResult

Returns the width of the data returned by the database for this query.

getWildCards() - Method in interface org.intermine.api.idresolution.JobInput

getWildCards() - Method in class org.intermine.web.logic.bag.WebJobInput

getWithinOptions() - Method in class org.intermine.api.query.range.AbstractHelper

getWorkingTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager

Fetch all user and global templates that are valid.

getWorkingTemplates() - Method in class org.intermine.api.template.TemplateManager

Fetch all global templates that are valid.

getWormIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a worm id resolver

getWormIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a worm id resolver

getWormIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService

Create a worm id resolver

getWriter() - Method in class org.intermine.webservice.server.output.StreamedOutput

Returns associated writer

getWrittenResultsCount() - Method in interface org.intermine.web.logic.export.Exporter

getWrittenResultsCount() - Method in class org.intermine.web.logic.export.ExporterImpl

getXAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget

getXml() - Method in class org.intermine.web.struts.ImportTagsForm

Get the xml.

getXml() - Method in class org.intermine.web.struts.ImportXMLForm

Get the xml.

getXML() - Method in class org.intermine.webservice.server.query.QueryUploadService

Get the XML which represents the queries to be saved.

getXml() - Method in class org.intermine.webservice.server.query.result.QueryResultInput

Gets xml query string.

getXMLSchemaUrl() - Method in class org.intermine.webservice.server.query.AbstractQueryService

getXref() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

getXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

used for testing

getXrefs() - Method in class org.intermine.bio.ontology.OboTerm

Get a set of xrefs (OboTerms) for this term.

getYAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget

GFF3Converter - Class in org.intermine.bio.dataconversion

Class to read a GFF3 source data and produce a data representation

GFF3Converter(ItemWriter, String, String, String, String, Model, GFF3RecordHandler, GFF3SeqHandler) - Constructor for class org.intermine.bio.dataconversion.GFF3Converter

Constructor

GFF3ConverterTask - Class in org.intermine.bio.task

Task to convert gff3 data

GFF3ConverterTask() - Constructor for class org.intermine.bio.task.GFF3ConverterTask

GFF3Parser - Class in org.intermine.bio.io.gff3

A parser for GFF3 files.

GFF3Record - Class in org.intermine.bio.io.gff3

A class that represents one line of a GFF3 file.

GFF3Record(String) - Constructor for class org.intermine.bio.io.gff3.GFF3Record

Create a GFF3Record from a line of a GFF3 file

GFF3Record(String, String, String, int, int, Double, String, String, Map<String, List<String>>) - Constructor for class org.intermine.bio.io.gff3.GFF3Record

Create a new GFF3Record

GFF3RecordHandler - Class in org.intermine.bio.dataconversion

Permits specific operations to be performed when processing an line of GFF3.

GFF3RecordHandler(Model) - Constructor for class org.intermine.bio.dataconversion.GFF3RecordHandler

Construct with the model to create items in (for type checking).

GFF3SeqHandler - Class in org.intermine.bio.dataconversion

An interface used by GFF3Converter to choose the type of sequence Items.

GFF3SeqHandler() - Constructor for class org.intermine.bio.dataconversion.GFF3SeqHandler

GFF3Util - Class in org.intermine.bio.web.export

Utility methods for GFF3.

GLOBAL - Static variable in class org.intermine.api.search.Scope

Global scope for public bags, templates, etc.

GLOBAL_BAGS - Static variable in class org.intermine.api.search.SearchTarget

The search target for global bags

GLOBAL_CACHE - Static variable in class org.intermine.web.logic.Constants

Servlet attribute.

GLOBAL_SEARCH_REPOSITORY - Static variable in class org.intermine.web.logic.Constants

Servlet attribute.

GLOBAL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget

The search target for global templates

GlobalRepository - Class in org.intermine.api.search

A representation of an object that knows how to index global objects, and also how to respond to changes to those objects.

GlobalRepository(Profile) - Constructor for class org.intermine.api.search.GlobalRepository

Build a new global search repository and register it with the list of global repositories available.

GLOBALS - Static variable in class org.intermine.api.search.SearchRepository

GoConverter - Class in org.intermine.bio.dataconversion

DataConverter to parse a go annotation file into Items

GoConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.GoConverter

Constructor

goFaster() - Method in class org.intermine.api.results.ExportResultsIterator

Switches on the goFaster mode in the objectstore for this query.

goFaster() - Method in class org.intermine.api.results.WebResults

Calls ObjectStore.goFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.

goFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Makes a certain Query go faster, using extra resources.

goFasterCacheMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

goFasterCountMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

goFasterMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

goFasterWithConnection(Query, Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Makes a certain Query go faster, using extra resources.

GoPostprocess - Class in org.intermine.bio.postprocess

Take any GOAnnotation objects assigned to proteins and copy them to corresponding genes.

GoPostprocess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.GoPostprocess

Create a new UpdateOrthologes object from an ObjectStoreWriter

GORNULL - Static variable in class org.intermine.sql.query.Constraint

An operation for this constraint indicating that the left is greater than the right, or the left is null.

goTerms - Variable in class org.intermine.bio.dataconversion.GoConverter

GotoWebSearchableAction - Class in org.intermine.web.struts

Action handles search.

GotoWebSearchableAction() - Constructor for class org.intermine.web.struts.GotoWebSearchableAction

grant(Database, String, String) - Static method in class org.intermine.sql.DatabaseUtil

Grant permission on all tables for given user on specified database.

grantPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager

Grant permission to the given identity, creating a profile for this identity if it is not already available.

GrantTask - Class in org.intermine.task

Task to grant permissions on all tables in a database to a given user.

GrantTask() - Constructor for class org.intermine.task.GrantTask

GRAPH_CACHE - Static variable in class org.intermine.web.logic.Constants

Servlet attribute.

GraphJSONProcessor - Class in org.intermine.webservice.server.widget

A widget result processor that produces chart results in JSON.

GraphService - Class in org.intermine.webservice.server.widget

GraphService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.GraphService

GraphWidget - Class in org.intermine.web.logic.widget

GraphWidget(GraphWidgetConfig, InterMineBag, ObjectStore, WidgetOptions) - Constructor for class org.intermine.web.logic.widget.GraphWidget

GraphWidget.DivNumberFormat - Class in org.intermine.web.logic.widget

class used to format the p-values on the graph

GraphWidget.DivNumberFormat(int) - Constructor for class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat

GraphWidgetActionType - Enum in org.intermine.web.logic.widget

Enumeration for possible actions when create the query for graph widgets.

GraphWidgetConfig - Class in org.intermine.web.logic.widget.config

Configuration object describing details of a graph displayer

GraphWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.GraphWidgetConfig

GraphWidgetLoader - Class in org.intermine.web.logic.widget

The class that does the actual querying for results.

GraphWidgetLoader(InterMineBag, ObjectStore, GraphWidgetConfig, String) - Constructor for class org.intermine.web.logic.widget.GraphWidgetLoader

Constructor.

GraphWidgetsServlet - Class in org.intermine.webservice.server.widget

Servlet running WidgetsService.

GraphWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.GraphWidgetsServlet

GraphXMLProcessor - Class in org.intermine.webservice.server.widget

A processor for returning results from graph widgets in XML.

GraphXMLProcessor() - Constructor for class org.intermine.webservice.server.widget.GraphXMLProcessor

Constructor, obvs

GREATER - Static variable in class org.intermine.sql.query.AbstractValue

Describes one AbstractValue as being greater than another AbstractValue.

greaterOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare this value of this AbstractValue with another to see if it is more or equal.

greaterThan(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be greater than a value.

greaterThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare this value of this AbstractValue with another to see if it is more.

greaterThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be greater than or equal to a value.

GREATEST - Static variable in class org.intermine.objectstore.query.QueryExpression

Return the greatest value from two expressions, e.g.

GREATEST - Static variable in class org.intermine.sql.query.Function

GREATEST(x, y) - takes two operands

groupBy - Variable in class org.intermine.sql.query.Query

groupByClass(Collection<E>, boolean) - Static method in class org.intermine.util.CollectionUtil

Sorts objects in the given collection into different types by Class.

H

handleCreation(CreationEvent) - Method in class org.intermine.api.search.GlobalRepository

handleCreation(CreationEvent) - Method in class org.intermine.api.search.SearchRepository

Respond in some way to the creation of a web searchable object.

handleCreation(CreationEvent) - Method in class org.intermine.api.search.UserRepository

handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.SearchRepository

Respond in some way to the deletion of a web searchable object.

handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.UserRepository

handleErrorResponse() - Method in class org.intermine.webservice.client.util.HttpConnection

Handles an error response received while executing a service request.

handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.HTMLTableFormatter

handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.XMLFormatter

Serialise the headers to the current string builder.

handleMassTagging() - Method in class org.intermine.api.search.GlobalRepository

handleMassTagging() - Method in class org.intermine.api.search.SearchRepository

Respond to the fact that multiple tags have been added and that we do not know what they are.

handleMassTagging() - Method in class org.intermine.api.search.UserRepository

handleMessages(BagQueryResult, HttpSession, Properties, String, String) - Static method in class org.intermine.web.struts.DisplayLookupMessageHandler

Generates and saves messages for bag lookup

handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.SearchRepository

Respond in some way to the change in the properties of a web searchable object.

handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.UserRepository

handlerClassName - Variable in class org.intermine.bio.task.GFF3ConverterTask

handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository

handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository

Respond in some way to the addition of a tag to a web searchable object.

handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.UserRepository

handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository

handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository

Respond in some way to the removal of a tag from a web searchable object.

handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.UserRepository

hasAllTags(Taggable) - Method in class org.intermine.api.search.TagFilter

Check to see if this taggable item has all the tags it is meant to.

hasAttribute(String) - Method in class org.intermine.xml.full.Item

Return true if named attribute exists.

hasAutocompleter(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter

checks if an autocompletion exists

hasBioSeg - Variable in class org.intermine.objectstore.intermine.DatabaseSchema

hasBioSeg() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if the database has the bioseg type installed.

hasCallback() - Method in class org.intermine.webservice.server.WebService

Determine whether a callback was supplied to this request.

hasClassName(String) - Method in class org.intermine.bio.dataconversion.IdResolver

Return true if the idResolver contains information about this class name.

hasCollection(String) - Method in class org.intermine.xml.full.Item

Return true if named collection exists.

hasComments() - Method in class org.intermine.bio.dataconversion.UniprotEntry

hasDatasetRefId() - Method in class org.intermine.bio.dataconversion.UniprotEntry

returns true if the protein has a dataset of SwissProt or Trembl.

HasFromList - Interface in org.intermine.objectstore.query

Interface to define the types of things that can have from elements added to them.

hashCode() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult

hashCode() - Method in class org.intermine.api.bag.SharingInvite

hashCode() - Method in class org.intermine.api.beans.ObjectDetails

hashCode() - Method in class org.intermine.api.beans.PartnerLink

hashCode() - Method in class org.intermine.api.idresolution.ResolutionJob

hashCode() - Method in class org.intermine.api.mines.ObjectRequest

hashCode() - Method in class org.intermine.api.mines.RemoteMine

hashCode() - Method in class org.intermine.api.profile.BagValue

hashCode() - Method in class org.intermine.api.profile.SavedQuery

Hash code.

hashCode() - Method in class org.intermine.api.results.Column

hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue

hashCode() - Method in class org.intermine.api.results.ResultElement

hashCode() - Method in class org.intermine.api.template.ApiTemplate

hashCode() - Method in class org.intermine.bio.chado.ChadoCVTerm

hashCode() - Method in class org.intermine.bio.ontology.OboTermSynonym

hashCode() - Method in class org.intermine.bio.util.OrganismData

hashCode() - Method in class org.intermine.objectstore.query.BagConstraint

hashCode() - Method in class org.intermine.objectstore.query.ClassConstraint

Get the hashCode for this object

hashCode() - Method in class org.intermine.objectstore.query.Clob

Override Object#hashCode.

hashCode() - Method in class org.intermine.objectstore.query.ConstraintSet

Get the hashCode for this object overrides Object.hashCode().

hashCode() - Method in class org.intermine.objectstore.query.ContainsConstraint

Get the hashCode for this object, overrides Object.hashCode()

hashCode() - Method in class org.intermine.objectstore.query.iql.IqlQuery

hashCode() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint

hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBag

Override Object#hashCode.

hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination

hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject

hashCode() - Method in class org.intermine.objectstore.query.OverlapConstraint

hashCode() - Method in class org.intermine.objectstore.query.PathExpressionField

hashCode() - Method in class org.intermine.objectstore.query.QueryCast

hashCode() - Method in class org.intermine.objectstore.query.QueryField

Returns a hash code for this object.

hashCode() - Method in class org.intermine.objectstore.query.QueryValue

Overrides Object.

hashCode() - Method in class org.intermine.objectstore.query.Results

hashCode() - Method in class org.intermine.objectstore.query.ResultsInfo

hashCode() - Method in class org.intermine.objectstore.query.SimpleConstraint

Get the hashCode for this object overrides Object.hashCode()

hashCode() - Method in class org.intermine.objectstore.query.SubqueryConstraint

Get the hashCode for this object overrides Object.hashCode()

hashCode() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint

Get the hashCode for this object overrides Object.hashCode()

hashCode() - Method in class org.intermine.pathquery.LogicExpression

hashCode() - Method in class org.intermine.pathquery.Node

hashCode() - Method in class org.intermine.pathquery.OrderElement

hashCode() - Method in class org.intermine.pathquery.Path

hashCode() - Method in class org.intermine.pathquery.PathQuery

hashCode() - Method in class org.intermine.sql.precompute.PrecomputedTable

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.AbstractConstraint

Overrides Object.hashcode();

hashCode() - Method in class org.intermine.sql.query.AbstractTable

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.query.AbstractValue

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.query.Constant

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.query.Constraint

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.ConstraintSet

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.ExplainResult

hashCode() - Method in class org.intermine.sql.query.Field

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.query.Function

Overrides Object.hashcode.

hashCode() - Method in class org.intermine.sql.query.InListConstraint

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.NotConstraint

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.OrderDescending

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.query.Query

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.SelectValue

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.SubQuery

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.SubQueryConstraint

Overrides Object.hashCode().

hashCode() - Method in class org.intermine.sql.query.Table

Overrides Object.hashcode().

hashCode() - Method in class org.intermine.sql.writebatch.Row

hashCode() - Method in class org.intermine.template.TemplateQuery

hashCode() - Method in class org.intermine.util.AlwaysMap

hashCode() - Method in class org.intermine.util.IdentityMap

hashCode() - Method in class org.intermine.util.ReferenceMap

hashCode() - Method in class org.intermine.web.logic.config.Displayer

hashCode() - Method in class org.intermine.web.logic.config.FieldConfig

hashCode() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart

hashCode() - Method in class org.intermine.web.logic.config.TableExportConfig

hashCode() - Method in class org.intermine.web.logic.config.Type

hashCode() - Method in class org.intermine.web.logic.config.WebConfig

hashCode() - Method in class org.intermine.web.logic.template.ConstraintInput

hashCode() - Method in class org.intermine.web.logic.TreeNode

hashCode() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

hashCode() - Method in class org.intermine.webservice.client.results.Item

hashCode() - Method in class org.intermine.webservice.client.results.Page

hashCode() - Method in class org.intermine.webservice.server.core.Either

hashCode() - Method in class org.intermine.webservice.server.core.Either.Left

hashCode() - Method in class org.intermine.webservice.server.core.Either.Right

hashCode() - Method in class org.intermine.webservice.server.JWTBuilder

hashCode() - Method in class org.intermine.xml.full.Attribute

hashCode() - Method in class org.intermine.xml.full.Item

hashCode() - Method in class org.intermine.xml.full.Reference

hashCode() - Method in class org.intermine.xml.full.ReferenceList

hashCodeNoUnion() - Method in class org.intermine.sql.query.Query

Returns a partial hashcode, ignoring other queries in the union.

hasHelperForType(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig

hashPassword(String) - Static method in class org.intermine.util.PasswordHasher

Converts a password into a hashed password, with a salt.

hasIssues() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues

hasKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper

For a given classreturn true if it has any identifying fields.

hasNext() - Method in class org.intermine.api.results.ExportResultsIterator

hasNext() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

hasNext() - Method in class org.intermine.util.CombinedIterator

hasNext() - Method in class org.intermine.util.ObjectPipe

hasNext() - Method in class org.intermine.util.SynchronisedIterator

hasNext() - Method in class org.intermine.webservice.server.core.TableRowIterator

hasNext() - Method in class org.intermine.webservice.server.output.FilteringResultIterator

hasNext() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator

hasNext() - Method in class org.intermine.webservice.server.output.JSONResultsIterator

hasNext() - Method in class org.intermine.webservice.server.output.JSONRowIterator

hasNext() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator

hasPrimaryAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry

some proteins don't have accessions.

hasProfile(String) - Method in class org.intermine.api.profile.ProfileManager

Check whether a user already has a Profile

hasReference(String) - Method in class org.intermine.xml.full.Item

Return true if named reference exists.

hasSeries() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

hasTag(String, Taggable) - Method in class org.intermine.api.profile.TagManager

Test whether a particular taggable thing has been tagged with a particular tag.

hasTag(String, Taggable, Profile) - Method in class org.intermine.api.profile.TagManager

Test whether a particular taggable thing has been tagged with a particular tag, by a particular user.

hasTaxon(String) - Method in class org.intermine.bio.dataconversion.IdResolver

Return true if the idResolver contains information about this taxon id.

hasTaxonAndClassName(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Check if resolver has taxon id and class name

hasTaxonAndClassNames(String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Check if resolver has taxon id and class name

hasTaxons(Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

Return true if the idResolver contains information about a collection of taxon id.

hasTaxonsAndClassName(Set<String>, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Check if resolver has taxon id and class name

hasTaxonsAndClassNames(Map<String, Set<String>>) - Method in class org.intermine.bio.dataconversion.IdResolver

Check if resolver has a set of keys (taxon id + class name)

hasValidPath(Object, String, InterMineAPI) - Static method in class org.intermine.web.logic.WebUtil

Check whether the runtime type of an object supports a particular path.

having - Variable in class org.intermine.sql.query.Query

HeaderConfigLink - Class in org.intermine.web.logic.config

Will store a link configured through HeaderConfig (WebConfig) and used on report page header

HeaderConfigLink() - Constructor for class org.intermine.web.logic.config.HeaderConfigLink

HeaderConfigTitle - Class in org.intermine.web.logic.config

Configuration of an object (Type) header when displayed on report

HeaderConfigTitle() - Constructor for class org.intermine.web.logic.config.HeaderConfigTitle

HeaderConfigTitle.TitlePart - Class in org.intermine.web.logic.config

Holder for a path that appears in the title and any prefix and suffix values if they have been configured.

HeaderFilter - Class in org.intermine.web.filters

A Filter that modifies response headers of outgoing pages.

HeaderFilter() - Constructor for class org.intermine.web.filters.HeaderFilter

HeartbeatAction - Class in org.intermine.web.struts

Takes a parameter "type" with value "webapp" or "query" and prints "OK" to the client if everything is ok, otherwise something else.

HeartbeatAction() - Constructor for class org.intermine.web.struts.HeartbeatAction

HgncIdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolver for HGNC previous symbols and aliases to current symbols.

HgncIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.HgncIdResolverFactory

Construct without SO term of the feature type.

HIDDEN - Static variable in class org.intermine.web.logic.Constants

The preference set if the user does not want to be found

hideColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Deprecated.

as we don't hide columns any more

HintingFetcher - Class in org.intermine.dataloader

Class providing EquivalentObjectFetcher functionality that makes use of hints to improve performance.

HintingFetcher(BaseEquivalentObjectFetcher) - Constructor for class org.intermine.dataloader.HintingFetcher

Constructor

HintManager - Class in org.intermine.web.logic.help

Hints are shown at the top of the pages in the web application, this class reads the hints in from properties and returns appropriate hints for a specified page.

HintManager(Properties) - Constructor for class org.intermine.web.logic.help.HintManager

Construct with the InterMine web properties, extract the configured hints and set up in an internal map.

HintsController - Class in org.intermine.web.struts

Executed for the hints tile that displays text information at the top of webapp pages.

HintsController() - Constructor for class org.intermine.web.struts.HintsController

HtmlHeadController - Class in org.intermine.web.struts

Controller for the html head tile.

HtmlHeadController() - Constructor for class org.intermine.web.struts.HtmlHeadController

htmlId - Variable in class org.intermine.api.results.ResultElement

HtmlListFormatter - Class in org.intermine.webservice.server.lists

A formatter that represents lists as HTML.

HtmlListFormatter() - Constructor for class org.intermine.webservice.server.lists.HtmlListFormatter

HTMLOutput - Class in org.intermine.webservice.server.output

HTMLOutput extends is similar to MemoryOutput, only difference is, that it prints out errors immediately to output.

HTMLOutput(PrintWriter) - Constructor for class org.intermine.webservice.server.output.HTMLOutput

Constructor.

HTMLTableFormatter - Class in org.intermine.webservice.server.output

A formatter that presents query results as HTML.

HTMLTableFormatter() - Constructor for class org.intermine.webservice.server.output.HTMLTableFormatter

HTMLWidget - Class in org.intermine.web.logic.widget

Represents a widget with no data, it just diplays the "content" string.

HTMLWidget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.HTMLWidget

HTMLWidgetConfig - Class in org.intermine.web.logic.widget.config

dummy widget to output html widget

HTMLWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.HTMLWidgetConfig

HttpClient - Class in org.intermine.web.util

Very simple http client that downloads data.

HttpClient() - Constructor for class org.intermine.web.util.HttpClient

HttpConnection - Class in org.intermine.webservice.client.util

The HttpConnection is class wrapping implementation details of http connection and the implementation can change easily.

HttpConnection(Request) - Constructor for class org.intermine.webservice.client.util.HttpConnection

HttpExporterBase - Class in org.intermine.web.logic.export.http

Abstract class with functionality common for all classes implementing TableHttpExporter interface like getting result from paged table.

HttpExporterBase() - Constructor for class org.intermine.web.logic.export.http.HttpExporterBase

HttpExportUtil - Class in org.intermine.web.logic.export.http

Util for export.

HttpRequester - Class in org.intermine.api.mines

A mine requester that makes HTTP requests.

HttpRequester() - Constructor for class org.intermine.api.mines.HttpRequester

Create an object that will make HTTP requests

HumanIdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolverFactory for human genes - tracking Ensembl ids, NCBI ids, HGNC ids, HGNC symbols.

HumanIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.HumanIdResolverFactory

Construct without SO term of the feature type.

HUNDRED - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

hyperLinkNote(String) - Static method in class org.intermine.task.AcceptanceTestTask

Return a hyperlinked version of the given note.

I

ID_ONLY - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

IDs only

IDENTIFIER_CONSTRAINT - Static variable in class org.intermine.api.config.Constants

constrain by object identifier

identifierToId(String) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Turn an item identifier into an object id.

IdentityMap<E> - Class in org.intermine.util

This is a dumb implementation of a Map.

idMap - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

idMap - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

idMapOps - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

IdResolutionService - Class in org.intermine.webservice.server.idresolution

IdResolutionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionService

Default constructor.

IdResolutionServlet - Class in org.intermine.webservice.server.idresolution

Route requests for ID resolution.

IdResolutionServlet() - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionServlet

IDResolver - Class in org.intermine.api.idresolution

IdResolver - Class in org.intermine.bio.dataconversion

Hold data about primary identifiers and synonyms for a particular class in the data model and provide methods to resolved synonyms into corresponding primary identifier(s).

IdResolver() - Constructor for class org.intermine.bio.dataconversion.IdResolver

Construct and empty IdResolver

IdResolver(String) - Constructor for class org.intermine.bio.dataconversion.IdResolver

Construct and empty IdResolver

idResolverCachedFileName - Static variable in class org.intermine.bio.dataconversion.IdResolverFactory

IdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolver.

IdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.IdResolverFactory

IdResolverService - Class in org.intermine.bio.dataconversion

A wrapper class to provide IdResolver service.

idToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Turn an object id into an item identifier.

idToNamespace - Variable in class org.intermine.dataconversion.ItemToObjectTranslator

IdUpgrader - Interface in org.intermine.api.bag

Bag object id upgrader - find old objects in a new ObjectStore.

ignore - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter

Should a character encoding specified by the client be ignored?

ignore - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

ignoreCombination(Map<Class<?>, Set<Class<?>>>, Class<?>, Class<?>) - Static method in class org.intermine.bio.postprocess.OverlapUtil

Return true if the given class should be ignored when overlapping with the other given class.

ignoreDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

ignoreDuplicates - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

ignoreDuplicates - Variable in class org.intermine.dataloader.XmlDataLoaderTask

ignoreNames - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

im - Variable in class org.intermine.web.displayer.ReportDisplayer

im - Variable in class org.intermine.web.logic.bag.BagConverter

im - Variable in class org.intermine.webservice.server.WebService

The configuration object.

IM_ASPECT_MISC - Static variable in class org.intermine.api.tag.TagNames

String used to tag objects by Miscellaneous aspect

IM_ASPECT_PREFIX - Static variable in class org.intermine.api.tag.TagNames

String used to tag objects by some aspect

IM_CONVERTER - Static variable in class org.intermine.api.tag.TagNames

String used to tag converter templates in the webapp.

IM_FAVOURITE - Static variable in class org.intermine.api.tag.TagNames

String used to tag favourite objects

IM_HIDDEN - Static variable in class org.intermine.api.tag.TagNames

String used to tag objects that should be hidden at jsp page

IM_PREFIX - Static variable in class org.intermine.api.tag.TagNames

Prefix common for all InterMine internal tags

IM_PUBLIC - Static variable in class org.intermine.api.tag.TagNames

Tag for pubic things (bags, templates).

IM_REPORT - Static variable in class org.intermine.api.tag.TagNames

String used to tag templates that should appear on report pages.

IM_SEARCH_RESULTS - Static variable in class org.intermine.api.tag.TagNames

templates to be displayed on search results page

IM_SUMMARY - Static variable in class org.intermine.api.tag.TagNames

String used to tag objects to appear in the summary section of the report page

IM_WIDGET - Static variable in class org.intermine.api.tag.TagNames

bag with background population for specific widget

immutable - Variable in class org.intermine.objectstore.query.Results

imObj - Variable in class org.intermine.api.results.ResultElement

IMPLIED_BY - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes one constraint as being implied by another constraint.

IMPLIES - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes one constraint as implying another constraint.

ImportQueriesAction - Class in org.intermine.web.struts

Imports query in XML format and forward user to the query builder.

ImportQueriesAction() - Constructor for class org.intermine.web.struts.ImportQueriesAction

ImportQueriesForm - Class in org.intermine.web.struts

Form bean representing query import form.

ImportQueriesForm() - Constructor for class org.intermine.web.struts.ImportQueriesForm

ImportTagsAction - Class in org.intermine.web.struts

Import tags.

ImportTagsAction() - Constructor for class org.intermine.web.struts.ImportTagsAction

ImportTagsForm - Class in org.intermine.web.struts

Form bean representing tags import form.

ImportTagsForm() - Constructor for class org.intermine.web.struts.ImportTagsForm

Creates a new instance of ImportTagsForm.

ImportXMLForm - Class in org.intermine.web.struts

Form bean representing a generic import form.

ImportXMLForm() - Constructor for class org.intermine.web.struts.ImportXMLForm

Construct a form.

in(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be IN a named bag.

INCOMPARABLE - Static variable in class org.intermine.sql.query.AbstractValue

Describes one AbstractValue as being incomparable to another AbstractValue.

IncompatibleTypes - Exception in org.intermine.api.bag.operations

IncompatibleTypes(MetaDataException) - Constructor for exception org.intermine.api.bag.operations.IncompatibleTypes

IncompatibleTypesException - Exception in org.intermine.api.bag

Exception thrown when given bags are of incompatible types, has methods to set and fetch the types.

IncompatibleTypesException(String) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException

Constructs an IncompatibleBagTypesException with the specified detail message.

IncompatibleTypesException(Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException

Constructs an IncompatibleBagTypesException with the specified nested throwable.

IncompatibleTypesException(String, Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException

Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.

incrementHintCount(String) - Method in class org.intermine.web.logic.results.WebState

Increment the number of times a hint has been displayed.

INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

INDENT - Static variable in class org.intermine.codegen.JavaModelOutput

INDENT - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput

INDENT2 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

INDENT3 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

indentXmlSimple(String) - Static method in class org.intermine.util.XmlUtil

Apply some indentiation to some XML.

INDEPENDENT - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as being independent.

index - Variable in class org.intermine.api.results.Column

INDEX_OF - Static variable in class org.intermine.objectstore.query.QueryExpression

Position of specified string in other specified string

indexes - Variable in class org.intermine.api.search.SearchRepository

indexOf(Object) - Method in class org.intermine.webservice.client.results.ResultRowList

indirections - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput

IndirectionTableBatch - Class in org.intermine.sql.writebatch

A class representing all changes to be made to an SQL indirection table.

IndirectionTableBatch(String, String) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch

Constructor for this class.

IndirectionTableBatch(String, String, Set<Row>) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch

Constructor for dodgy temp table deleting stuff

inferExperimentType(Set<String>, String) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Work out an experiment type give the combination of protocols used for the submission.

info - Variable in class org.intermine.objectstore.query.ResultsBatches

informUserOfNewSharedBag(String, Profile, InterMineBag) - Method in class org.intermine.util.Emailer

Send a 'sharing list' message

inIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be IN a collection of ids.

init() - Method in class org.intermine.objectstore.query.ClobAccess

Initialises the state of this object.

init(FilterConfig) - Method in class org.intermine.web.filters.ExpiresHeaderFilter

Initialise this Filter.

init(FilterConfig) - Method in class org.intermine.web.filters.HeaderFilter

Initialise this Filter.

init(FilterConfig) - Method in class org.intermine.web.filters.ReleaseEtagFilter

init(FilterConfig) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter

Place this filter into service.

init(ServletConfig) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator

init(ActionServlet, ModuleConfig) - Method in class org.intermine.web.struts.InitialiserPlugin

Init method called at Servlet initialisation

init() - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet

init() - Method in class org.intermine.webservice.server.core.RestfulServlet

init(FilterConfig) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter

init(ServletConfig) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet

init() - Method in class org.intermine.webservice.server.lists.ListInput

Initialise this structure

initialise(InterMineAPI, Properties, WebConfig, ResourceOpener) - Static method in class org.intermine.web.context.InterMineContext

Set up the Context with everything it needs.

initialise() - Method in class org.intermine.web.struts.BagUploadConfirmForm

Initialise the form.

initialise() - Method in class org.intermine.web.struts.ChangeTableSizeForm

Initialiser

initialise() - Method in class org.intermine.web.struts.CSVExportForm

Initialiser

initialise() - Method in class org.intermine.web.struts.EnrichmentWidgetForm

Initialiser

initialise() - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Initialiser

initialise() - Method in class org.intermine.web.struts.ModifyBagForm

Initialiser

initialise() - Method in class org.intermine.web.struts.ModifyQueryForm

Initialiser

initialise() - Method in class org.intermine.web.struts.ModifySuperUserForm

Initialiser

initialise() - Method in class org.intermine.web.struts.ModifyTemplateForm

Initialiser

initialise() - Method in class org.intermine.web.struts.SaveBagForm

Initialiser

initialise() - Method in class org.intermine.web.struts.TableExportForm

Initialiser

initialise() - Method in class org.intermine.web.struts.TriageBagForm

initialise() - Method in class org.intermine.web.struts.WidgetForm

Initialiser

initialiseCommonFeatures(Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Initialise SequenceProcessor with features that have already been processed and put the same features data into a commonFeaturesMap that tracks features (e.g.

initialised - Variable in class org.intermine.objectstore.query.ResultsBatches

initialiseDelendumAccumulator(Set<String>, ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService

Initialise the accumulator that builds up the list of temporary lists to delete.

initialiseFeatureMap(Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Initialise FeatureMap with features that have already been processed.

initialiseMapsForFile() - Method in class org.intermine.bio.dataconversion.GoConverter

Reset maps that don't need to retain their contents between files.

INITIALISER_KEY_ERROR - Static variable in class org.intermine.web.logic.Constants

Key for the initialiser error

InitialiserPlugin - Class in org.intermine.web.struts

Initialiser for the InterMine web application.

InitialiserPlugin() - Constructor for class org.intermine.web.struts.InitialiserPlugin

initKeywordSearch(InterMineAPI, String) - Static method in class org.intermine.api.lucene.KeywordSearch

loads or creates the lucene index

initSession(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Initialise a new session.

initState() - Method in class org.intermine.webservice.server.model.ModelService

initState() - Method in class org.intermine.webservice.server.path.PossibleValuesService

initState() - Method in class org.intermine.webservice.server.query.result.QueryResultService

initState() - Method in class org.intermine.webservice.server.VersionService

initState() - Method in class org.intermine.webservice.server.WebService

Subclasses can put initialisation here.

initUserProfileResources(ObjectStoreWriter) - Method in class org.intermine.api.InterMineAPI

Initialise parts of this object that require connection to a user-profile object store.

INLINE_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants

The name of the property to look up to find the maximum size of an inline table.

InlineList - Class in org.intermine.web.logic.results

InlineList(Set<Object>, String, Boolean, String, Integer) - Constructor for class org.intermine.web.logic.results.InlineList

Set a set ;) of Objects by turning them into InterMineObjects and then InlineListObjects

InlineListConfig - Class in org.intermine.web.logic.config

Represents an inline list to be shown on a Report page

InlineListConfig() - Constructor for class org.intermine.web.logic.config.InlineListConfig

InlineListObject - Class in org.intermine.web.logic.config

An individual InterMineObject wrapped in an InlineList Set

InlineListObject(InterMineObject, Object, Object) - Constructor for class org.intermine.web.logic.config.InlineListObject

Initialize

InlineResultsTable - Class in org.intermine.web.logic.results

An inline table created from a Collection This table has one object per row

InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.InlineResultsTable

Construct a new InlineResultsTable object

InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>, String, FieldDescriptor) - Constructor for class org.intermine.web.logic.results.InlineResultsTable

Construct with parent type and a field descriptor.

InlineResultsTableRow - Class in org.intermine.web.logic.results

Provides a wrapper for a row of InlineTableResultElement

InlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.InlineResultsTableRow

InlineTableResultElement - Class in org.intermine.web.logic.results

ResultElement used in an InlineResultsTable

InlineTableResultElement(FastPathObject, Path, FieldConfig, Boolean) - Constructor for class org.intermine.web.logic.results.InlineTableResultElement

Instantiate ResultElement while saving its FieldConfig

InlineTagEditorController - Class in org.intermine.web.struts

Controller for the inline tag editing tile

InlineTagEditorController() - Constructor for class org.intermine.web.struts.InlineTagEditorController

InListConstraint - Class in org.intermine.sql.query

A representation of a constraint where an AbstractValue is IN a list of constants.

InListConstraint(AbstractValue) - Constructor for class org.intermine.sql.query.InListConstraint

Constructor for InListConstraint object.

inputModelFile - Variable in class org.intermine.task.ModelMergerTask

insertCollectionField(String, String, String, String, String, String, boolean) - Method in class org.intermine.bio.postprocess.CreateReferences

Add a collection of objects of type X to objects of type Y by using a connecting class.

insertReferenceField(String, String, String, String, String, String) - Method in class org.intermine.bio.postprocess.CreateReferences

Add a reference to and object of type X in objects of type Y by using a connecting class.

insertReferences() - Method in class org.intermine.bio.postprocess.CreateReferences

Fill in missing references/collections in model by querying relations

INSTANCE - Static variable in class org.intermine.pathquery.PathQueryBinding

A single instance of this class

INSTANCE - Static variable in class org.intermine.template.xml.TemplateQueryBinding

A single instance of this class

instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor

instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor

instance() - Static method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor

instance() - Static method in class org.intermine.webservice.server.widget.FlatWidgetProcessor

instance() - Static method in class org.intermine.webservice.server.widget.GraphJSONProcessor

instance() - Static method in class org.intermine.webservice.server.widget.JSONWidgetProcessor

instance() - Static method in class org.intermine.webservice.server.widget.TableJSONProcessor

instance() - Static method in class org.intermine.webservice.server.widget.TableXMLProcessor

instance() - Static method in class org.intermine.webservice.server.widget.XMLWidgetProcessor

instances - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

instances - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager

instantiateObject(String, String) - Static method in class org.intermine.util.DynamicUtil

Create an outline business object from a class name and a list of interface names

INT_BAG_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the table that holds the integer ObjectStoreBag elements.

IntegrationWriter - Interface in org.intermine.dataloader

Define methods needed to deal with integration when writing to an ObjectStore.

integrationWriter - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

integrationWriter - Variable in class org.intermine.dataloader.XmlDataLoaderTask

IntegrationWriterAbstractImpl - Class in org.intermine.dataloader

Abstract implementation of ObjectStoreIntegrationWriter.

IntegrationWriterAbstractImpl(ObjectStoreWriter) - Constructor for class org.intermine.dataloader.IntegrationWriterAbstractImpl

Constructs a new instance of an IntegrationWriter

IntegrationWriterDataTrackingImpl - Class in org.intermine.dataloader

Priority-based implementation of IntegrationWriter.

IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Constructs a new instance of IntegrationWriterDataTrackingImpl.

IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker, Set<Class<?>>) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Constructs a new instance of IntegrationWriterDataTrackingImpl.

IntegrationWriterFactory - Class in org.intermine.dataloader

Produce IntegrationWriters

intercept(Object, Method, Object[], MethodProxy) - Method in class org.intermine.util.DynamicBean

Intercept all method calls, and operate on Map.

IntergenicRegionUtil - Class in org.intermine.bio.postprocess

Methods for creating feature for intergenic regions.

IntergenicRegionUtil(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.IntergenicRegionUtil

Create a new IntergenicRegionUtil object that will operate on the given ObjectStoreWriter.

INTERMINE_API - Static variable in class org.intermine.web.logic.Constants

Key for the InterMine API object

INTERMINE_VERSION - Static variable in class org.intermine.web.logic.Constants

Current version of the InterMine code

InterMineAction - Class in org.intermine.web.struts

An InterMine specific version of Action.

InterMineAction() - Constructor for class org.intermine.web.struts.InterMineAction

InterMineAPI - Class in org.intermine.api

InterMineAPI provides access to manager objects for the main parts of an InterMine application: the production ObjectStore, the userprofile (via ProfileManager), template queries, bags and tags.

InterMineAPI() - Constructor for class org.intermine.api.InterMineAPI

Protected no-argument constructor only used for building test implementations of this class.

InterMineAPI(ObjectStore, ObjectStoreWriter, ClassKeys, BagQueryConfig, ObjectStoreSummary, TrackerDelegate, LinkRedirectManager) - Constructor for class org.intermine.api.InterMineAPI

Construct an InterMine API object.

InterMineBag - Class in org.intermine.api.profile

An object that represents a bag of objects in our database for the webapp.

InterMineBag(String, String, String, Date, BagState, ObjectStore, Integer, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag

Constructs a new InterMineIdBag, and saves it in the UserProfile database.

InterMineBag(String, String, String, Date, BagState, ObjectStore, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag

Constructs a new InterMineBag, and saves it in the UserProfile database.

InterMineBag(ObjectStore, Integer, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InterMineBag

Loads an InterMineBag from the UserProfile database.

InterMineBag(ObjectStore, Integer, ObjectStoreWriter, boolean) - Constructor for class org.intermine.api.profile.InterMineBag

Loads an InterMineBag from the UserProfile database.

InterMineBagBinding - Class in org.intermine.api.xml

Parse InterMineIdBags in XML format

InterMineBagBinding() - Constructor for class org.intermine.api.xml.InterMineBagBinding

InterMineBagHandler - Class in org.intermine.api.xml

A handler for turning XML bags data into an InterMineIdBag.

InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>, Integer) - Constructor for class org.intermine.api.xml.InterMineBagHandler

Create a new InterMineBagHandler object.

InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>) - Constructor for class org.intermine.api.xml.InterMineBagHandler

Create a new InterMineBagHandler object.

InterMineContext - Class in org.intermine.web.context

A context object that doesn't require the session.

InterMineDispatchAction - Class in org.intermine.web.struts

An InterMine specific version of DispatchAction.

InterMineDispatchAction() - Constructor for class org.intermine.web.struts.InterMineDispatchAction

InterMineExceptionHandler - Class in org.intermine.web.struts

InterMine implementation of the Struts ExceptionHandler

InterMineExceptionHandler() - Constructor for class org.intermine.web.struts.InterMineExceptionHandler

InterMineLinkGenerator - Interface in org.intermine.web.displayer

Helper class for intermine links generated on report and list pages

InterMineLinkGenerator - Class in org.intermine.web.util

Helper class for intermine links generated on report and list pages

InterMineLinkGenerator() - Constructor for class org.intermine.web.util.InterMineLinkGenerator

InterMineLookupDispatchAction - Class in org.intermine.web.struts

An InterMine specific version of LookupDispatchAction.

InterMineLookupDispatchAction() - Constructor for class org.intermine.web.struts.InterMineLookupDispatchAction

InterMineObject - Interface in org.intermine.model

A root interface for all objects that can be stored in a InterMine database.

InterMineObjectFetcher - Class in org.intermine.api.lucene

thread to fetch all intermineobjects (with exceptions) from database, create a lucene document for them, add references (if applicable) and put the final document in the indexing queue

InterMineObjectFetcher(ObjectStore, Map<String, List<FieldDescriptor>>, ObjectPipe<Document>, Set<Class<? extends InterMineObject>>, Map<Class<? extends InterMineObject>, Set<String>>, Map<Class<? extends InterMineObject>, String[]>, Map<ClassDescriptor, Float>, Vector<KeywordSearchFacetData>, Map<String, String>) - Constructor for class org.intermine.api.lucene.InterMineObjectFetcher

initialize the documentfetcher thread

InterMineRequestProcessor - Class in org.intermine.web.struts

A RequestProcessor that sends you back to the start if your session isn't valid.

InterMineRequestProcessor() - Constructor for class org.intermine.web.struts.InterMineRequestProcessor

InternalBagOperationException - Exception in org.intermine.api.bag.operations

Exceptions that are the fault of underlying infrastructure, and not the way the classes themselves were used. ie.

InternalBagOperationException() - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException

Constructor

InternalBagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException

InternalBagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException

InternalBagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException

internalCompare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet

Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.

InternalErrorException - Exception in org.intermine.webservice.client.exceptions

The InternalErrorException is thrown by service when an error occurred at the server.

InternalErrorException(String) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException

InternalErrorException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException

InternalErrorException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException

InternalErrorException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException

internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Internal service method for getObjectById.

internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Internal service method for getObjectById.

internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Internal service method for getObjectById.

internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Internal service method for getObjectById.

internalGetObjectByIdWithConnection(Connection, Integer, Class<?>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Gets an object by id given a Connection.

interpretFormat(String) - Static method in class org.intermine.webservice.server.WebServiceRequestParser

Figure out which format the user wants.

InterProConverter - Class in org.intermine.bio.dataconversion

DataConverter to parse InterPro data into items

InterProConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.InterProConverter

Constructor

INTERSECT - Static variable in class org.intermine.api.bag.BagOperations

Constant representing logical intersection.

intersect(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations

Create a bag that is the INTERSECTION of all the bags provided, if the intersection is the empty set then don't create the new bag.

INTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination

Constant representing an INTERSECTION operation

intersect(ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Intersect one or more lists to produce a new list.

intersect(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Intersect one or more lists to produce a new list.

intersect(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Intersect one or more lists to produce a new list.

intersect(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Intersect one or more lists to produce a new list.

Intersection - Class in org.intermine.api.bag.operations

Intersection(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Intersection

IntHelper - Class in org.intermine.api.query.range

IntHelper() - Constructor for class org.intermine.api.query.range.IntHelper

IntPresentSet - Class in org.intermine.util

This is a set of ints.

IntPresentSet() - Constructor for class org.intermine.util.IntPresentSet

Constructor for this class.

intronMap - Variable in class org.intermine.bio.postprocess.IntronUtil

intronTranscripts - Variable in class org.intermine.bio.postprocess.IntronUtil

IntronUtil - Class in org.intermine.bio.postprocess

Methods for creating feature for introns.

IntronUtil(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.IntronUtil

Create a new IntronUtil object that will operate on the given ObjectStoreWriter.

IntToIntMap - Class in org.intermine.util

This is a map that maps from int to int.

IntToIntMap() - Constructor for class org.intermine.util.IntToIntMap

Constructor for this class.

INVALID_NAME_MSG - Static variable in class org.intermine.api.profile.TagManager

What we tell users when they give us an invalid tag name

INVALID_NAME_MSG - Static variable in class org.intermine.api.util.NameUtil

error message for bad names.

INVALID_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

invalidate() - Method in class org.intermine.api.profile.InterMineBag

Declare that this bag is invalid, and return its InvalidBag representation.

invalidateBagTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods

Remove a cached bag table from the session.

invalidateObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Removes an entry from the objectstore getObjectById cache.

invalidateObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore

Removes an entry from the objectstore getObjectById cache.

invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Removes an entry from the objectstore getObjectById cache.

invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Removes an entry from the objectstore getObjectById cache.

InvalidBag - Class in org.intermine.api.profile

A class representing a bag that is invalid because it does not conform to the current model.

InvalidBag(String, String, String, Date, ObjectStore, Integer, Integer, ObjectStoreBag, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag

Constructor.

InvalidBag(String, String, String, Date, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag

Minimal constructor.

InvalidBag(SavedBag, Integer, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag

Constructor callable by the ProfileManager.

InvalidQueryException - Exception in org.intermine.api.query.codegen

A class representing a failure to generate the code for a query because the query is invalid.

InvalidQueryException(String) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException

Construct an exception with a single problem.

InvalidQueryException(Collection<? extends String>) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException

Construct an exception with a list of problems.

InvitationAction - Class in org.intermine.web.struts

Action that processes invitations.

InvitationAction() - Constructor for class org.intermine.web.struts.InvitationAction

InvitationForm - Class in org.intermine.web.struts

A form that contains the information for requests that invite users to share resources.

InvitationForm() - Constructor for class org.intermine.web.struts.InvitationForm

InvitationHandler - Class in org.intermine.api.bag

InvitationHandler() - Constructor for class org.intermine.api.bag.InvitationHandler

inviteToShare(InterMineBag, String) - Static method in class org.intermine.api.bag.SharedBagManager

Generate an invitation to share a bag.

invokeConstructor(ClobAccess) - Method in class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory

Method to return a new instance of the subclass of ClobAccess that this object represents.

IqlQuery - Class in org.intermine.objectstore.query.iql

OQL representation of an object-based Query

IqlQuery() - Constructor for class org.intermine.objectstore.query.iql.IqlQuery

No-arg constructor (for deserialization)

IqlQuery(String, String, List<?>) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery

Construct an IQL query from a String.

IqlQuery(String, String) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery

Construct an IQL query from a String.

IqlQuery(Query) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery

Construct an IQL query from a Query object.

IqlQueryParser - Class in org.intermine.objectstore.query.iql

Parser for the InterMine dialect of OQL (IQL)

IS_SUPERUSER - Static variable in class org.intermine.web.logic.Constants

Session attribute equals Boolean.TRUE when logged in user is superuser.

isa(String) - Method in class org.intermine.webservice.client.results.Item

Determine whether this item belongs to the class of objects of the named type.

isAggregate() - Method in class org.intermine.sql.query.AbstractValue

Returns true if this value is an aggregate function.

isAggregate() - Method in class org.intermine.sql.query.Constant

Returns true if this value is an aggregate function.

isAggregate() - Method in class org.intermine.sql.query.Field

Returns true if this value is an aggregate function.

isAggregate() - Method in class org.intermine.sql.query.Function

Returns true if this value is an aggregate function.

isAggregate() - Method in class org.intermine.sql.query.OrderDescending

Returns true if this value is an aggregate function.

isAllRowsSelected() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return true if a whole column is selected either by selecting the whole column checkbox or by selecting each row individually.

isAnyBagInState(Profile, BagState) - Method in class org.intermine.api.bag.BagManager

Return true if there is at least one user bag for the given profile in the given state

isAnyBagInStates(Profile, Set<BagState>) - Method in class org.intermine.api.bag.BagManager

Return true if there is at least one user bag for the given profile in at least one of the given states

isAnyBagNotCurrent(Profile) - Method in class org.intermine.api.bag.BagManager

Return true if there is at least one user bag for the given profile in the 'not_current' state.

isAnyBagNotCurrentOrUpgrading(Profile) - Method in class org.intermine.api.bag.BagManager

Return true if there is at least one user bag for the given profile in the 'not_current' state or 'upgrading'.

isAnyBagToUpgrade(Profile) - Method in class org.intermine.api.bag.BagManager

Return true if there is at least one user bag for the given profile in the 'to_upgrade' state.

isAnyBagUnresolvable() - Method in class org.intermine.webservice.server.core.ListManager

Return true if there is at least one bag in the 'to_upgrade' state.

isApplicable() - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Return true if the correction coefficient is applicable

isAspectTag(String) - Static method in class org.intermine.api.tag.AspectTagUtil

isAssignableFrom(Class<?>, Class<?>) - Static method in class org.intermine.util.DynamicUtil

Returns true if sup is a superclass of sub (or the same), taking into account dynamic classes.

isAssociatedWith(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Returns true if the constraint is associated with the given FromElement.

isAssociatedWithNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Returns true if the given constraint is associated with no particular FromElement.

isAttribute() - Method in class org.intermine.pathquery.Node

Gets the value of attribute

isAttribute() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns true if the path represents an attribute (rather than a class, reference, or collection).

isAuthenticated() - Method in class org.intermine.webservice.server.WebService

isAuthorized() - Method in class org.intermine.webservice.client.lists.ItemList

isBagConstraint() - Method in class org.intermine.template.TemplateValue

Return true if this constraint value is a bag.

isBagSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and a bag has been selected.

isBagValuesEmpty(Connection) - Static method in class org.intermine.sql.DatabaseUtil

Verify if 'bagvalues' table is empty

isBoolean() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing having the attribute type boolean or Boolean

isCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Find out whether the query was cancelled.

isCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Find out whether an error occured while trying to run the query.

isCellValidForPath(ResultElement, Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Test whether a result element matches the type of its path.

isChart() - Method in class org.intermine.webservice.client.widget.Widget

isCollection() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns true if the reference is a collection.

isCollection() - Method in class org.intermine.pathquery.Node

Gets the value of collection

isCollection() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns true if the path represents a collection.

isComplement(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask

Return true if and only if the given location string represents a location on the reverse strand.

isCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Find out whether the query has completed.

isComputeTotalCount() - Method in class org.intermine.webservice.server.query.result.QueryResultInput

Returns true if should be displayed total count of all available results.

isConsistentType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag

isCountRequest(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser

isCrossReference(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Returns true if the Constraint is a cross-reference between two QueryClasses.

isCurrent() - Method in class org.intermine.api.profile.InterMineBag

Return true if the status bag is current, otherwise false (status is not current or to upgrade)

isDeleteTracks() - Method in class org.intermine.web.struts.TemplatesImportForm

Get the deleteTracks flag.

isDirect() - Method in class org.intermine.bio.ontology.OboRelation

isDirty() - Method in class org.intermine.dataloader.ObjectDescription

Returns whether this ObjectDescription is dirty.

isDisabled() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the constraint is disabled, false if it is enabled or locked.

isDistinct() - Method in class org.intermine.objectstore.query.Query

Get the value of the distinct property

isDistinct() - Method in class org.intermine.sql.query.Query

Gets the current distinct status of this query.

isDuplicate() - Method in class org.intermine.bio.dataconversion.UniprotEntry

isDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

isEditable(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Returns whether a constraint is editable.

isEditable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Get the editable flag (when building a template).

isEditableInTemplate() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing template constraint and that constraint is editable.

isEditableInTemplate() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Returns true if the constraint is part of a template query and the constraint is editable in that template.

isEdited() - Method in class org.intermine.template.TemplateQuery

Returns true if the TemplateQuery has been edited by the user and is therefore saved only in the query history.

isEmpty() - Method in class org.intermine.objectstore.query.Results

isEmpty(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Returns true is there are no rows in the results.

isEmpty() - Method in class org.intermine.pathquery.PathQuery

Returns true if the query has no features yet.

isEmpty() - Method in class org.intermine.util.AlwaysMap

isEmpty() - Method in class org.intermine.util.IdentityMap

isEmpty() - Method in class org.intermine.util.PseudoSet

isEmpty() - Method in class org.intermine.util.ReferenceMap

isEmpty() - Method in class org.intermine.web.logic.results.DisplayField

Return true if the collection is empty or reference null.

isEmpty() - Method in class org.intermine.webservice.client.results.ResultRowList

isEmptySelection() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return true if and only if nothing is selected

isEnabled() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the constraint is enabled, false if it is disabled or locked.

isEnrichment() - Method in class org.intermine.webservice.client.widget.Widget

isErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods

Return true if exists blocking errors

isExplain() - Method in class org.intermine.sql.query.Query

Gets the current explain status of this query.

isExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if this is a LOOKUP constraint and an extra constraint should be available.

isFetchFromInterMineObject() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if ProxyReferences can be fetched from the InterMineObject table.

isFilterConstraint(WidgetConfig, PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil

isFirstPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Check if were are on the first page

isFlatMode(Class<?>) - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if the ObjectStore needs to run in flat mode for this Class - if notXml is missing and the InterMineObject table is missing (or if the class is not a subclass of InterMineObject).

isForcedInnerJoin() - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Return true if this path is forced to be an inner join because it is involved in a loop constraint.

isFragment() - Method in class org.intermine.bio.dataconversion.UniprotEntry

isGzip() - Method in class org.intermine.webservice.server.WebService

isInputFieldDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the input field can be displayed, method for use in JSP

isInRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

True if the permission granted includes access to this role.

isInstance(Model, InterMineObject, String) - Static method in class org.intermine.bio.postprocess.PostProcessUtil

Convenience method to test whether an InterMineObject is an instance of the given class name without needing to import the class itself.

isInstance(Object, Class<?>) - Static method in class org.intermine.util.DynamicUtil

Returns true if obj is an instance of clazz, taking into account dynamic classes.

isInTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Check whether the ObjectStore is performing a transaction, delegate to internal ObjectStoreWriter.

isInTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Check whether the ObjectStoreWriter is performing a transaction

isInTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter

Check whether the ObjectStoreWriter is performing a transaction

isInTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Finds if we are in a transaction.

isInvalidTemplate(WebSearchable) - Static method in class org.intermine.api.search.SearchResults

Check if a websearchable is an invalid template.

isIsoform() - Method in class org.intermine.bio.dataconversion.UniprotEntry

isIssues() - Method in class org.intermine.web.struts.DisplayLookupMessageHandler

Check if there are any identifiers that didn't match.

isJsonP(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser

Work out if this a JSON-P request.

isKeyField(Map<String, List<FieldDescriptor>>, String, String) - Static method in class org.intermine.api.config.ClassKeyHelper

For a given class/field return true if it is an 'identifying' field.

isKeyField() - Method in interface org.intermine.api.results.ResultCell

isKeyField() - Method in class org.intermine.api.results.ResultElement

Return true if this object represents a field that is an identifying field (according to ClassKeyHelper.isKeyField())

isKeyField() - Method in class org.intermine.webservice.server.core.TableCell

isLastPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Check if we are on the last page

isLeaf() - Method in class org.intermine.web.logic.TreeNode

Is this node a leaf?

isLegalColumnName(String) - Static method in class org.intermine.sql.DatabaseUtil

Check that a column name provided to us is a legal column name, to prevent SQL injection.

isListConstraint(PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil

isListPathSet() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

isLocal() - Method in class org.intermine.api.profile.Profile

Returns true if this is a local account, and not, for example, an OpenID account.

isLocked() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the constraint is locked, it should'n be enabled or disabled.

isLocked() - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Return true if this path is locked because it is involved in a loop constraint.

isLoggedIn() - Method in class org.intermine.api.profile.Profile

Return true if and only if the user is logged is (and the Profile will be written to the userprofile).

isLoggedIn() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

isLoggedIn() - Method in class org.intermine.api.util.AnonProfile

isLookup() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if this constraint should be a LOOKUP, true if constraining a class (ref/col) instead of an attribute and that class has class keys defined.

isLoopSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and a loop value has been selected.

isMissingNotXml() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if NotXML should be omitted from all tables except the InterMineObject table, and the InterMineObject table is present.

isMultiConnection() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultiConnection() - Method in interface org.intermine.objectstore.ObjectStore

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultiConnection() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultiConnection() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.

isMultipleValue() - Method in class org.intermine.template.TemplateValue

isMultiValue() - Method in class org.intermine.webservice.client.template.TemplateParameter

isMultiValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the multi-select containing the possibleValue can be displayed, method for use in JSP

isMultiValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and a multivalue has been selected.

isNextEnabled() - Method in class org.intermine.web.tags.table.NavigationBarTag

isNotNull(String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be not null.

isNull(String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be null.

isNullSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and 'has a value' or 'has no value' has been selected.

ISO8601DateFormat - Class in org.intermine.webservice.server.core

A date formatter for the ISO8601 date format.

ISO8601DateFormat() - Constructor for class org.intermine.webservice.server.core.ISO8601DateFormat

Constructor.

ISO_DATE_FORMAT - Static variable in class org.intermine.pathquery.ConstraintValueParser

A date format for ISO dates.

isObjectConstraint() - Method in class org.intermine.template.TemplateValue

Return true if this constraint value is on InterMineObject

isObsolete() - Method in class org.intermine.bio.ontology.OboTerm

Return the obsolete flag for this term.

isOfType(String) - Method in class org.intermine.api.profile.InterMineBag

Test whether the given type can be added to this bag, type can be a qualified or un-qualified string.

isOnlyAttribute() - Method in class org.intermine.pathquery.Path

Return true if the Path does not contain references or collections

isOpen() - Method in class org.intermine.web.logic.TreeNode

Is this node expanded?

isOpenByDefault() - Method in class org.intermine.web.logic.config.FieldConfig

Get whether this field should be uncollapsed if sectionOnRight is true.

isOpened() - Method in class org.intermine.webservice.client.util.HttpConnection

isOptional(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Returns whether a constraint is optional.

isOuterJoin() - Method in class org.intermine.pathquery.Node

Returns true if this should be an outer join.

isOverwriting() - Method in class org.intermine.web.struts.ImportTagsForm

Get the overwrite flag.

isOverwriting() - Method in class org.intermine.web.struts.TemplatesImportForm

Get the overwrite flag.

isPathCompletelyInner(String) - Method in class org.intermine.pathquery.PathQuery

Returns true if a path string is in the root outer join group of this query.

isPathContainingSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil

Check to see if the path contains a subclass.

isPossibleValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if the drop-down containing the possibleValues can be displayed, method for use in JSP

isPrecomputed(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Checks if a query is precomputed or not for the given type

isPrecomputedWithConnection(Connection, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Checks if a query is precomputed or not for the given type and connection

isPrimaryIdentifier(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Check whether the given id is a primary identifier for this taxonId

isPrimaryIdentifier(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

Check whether the given id is a primary identifier for this taxonId

isPrimitive() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Return true if the end element of the path is an attribute and the attribute is a primitive type.

isProfileCached(String) - Method in class org.intermine.api.profile.ProfileManager

Check if the profile, whose username is given in input, has been cached by the profile cache

isPublic(InterMineBag) - Method in class org.intermine.api.bag.BagManager

Return true if the bag is public.

isPublic() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

Returns whether this query is publicly accessible.

isRangeSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and a range has been entered.

isRedundant() - Method in class org.intermine.bio.ontology.OboRelation

isReference() - Method in class org.intermine.pathquery.Node

Gets the value of reference

isReference() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns true if the path represents a reference.

isRelatedTo(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Returns true if the constraint is associated with the given FromElement.

isRelatedToNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Returns true if the given constraint is related to no FromElement.

isRequired(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Returns whether a constraint is required.

isReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Returns true if the given String is an IQL reserved word.

isReverseReference() - Method in class org.intermine.web.logic.query.MetadataNode

Returns true if this path is a reverse reference back onto the previous node.

isRO() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

isRootPath() - Method in class org.intermine.pathquery.Path

Return true if this path represents just the starting class, e.g.

isRW() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission

isSectionOnRight() - Method in class org.intermine.web.logic.config.FieldConfig

Whether this field should be rendered in its own section on the right side of the page.

isSelectable() - Method in class org.intermine.api.results.Column

Gets the value of selectable

isSelected() - Method in class org.intermine.web.logic.query.MetadataNode

Get the value of selected

isSelected() - Method in class org.intermine.web.logic.TreeNode

Is this node selected?

isSelected(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Return true if the correction coefficient is selected

isShowExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint

isSingleBatch() - Method in class org.intermine.api.results.WebResults

Returns true if the results are known to be contained in a single batch.

isSingleBatch() - Method in interface org.intermine.api.results.WebTable

Returns true if the results are known to be contained in a single batch.

isSingleBatch() - Method in class org.intermine.objectstore.query.Results

Returns true if the results are known to fit entirely within the first batch.

isSingleBatch() - Method in class org.intermine.objectstore.query.ResultsBatches

Returns true if the results are known to fit entirely within the first batch.

isSingleton() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Returns true if the SELECT list is empty or if singleton results are requested.

isSizeEstimate() - Method in class org.intermine.api.results.WebResults

Check whether the result of getEstimatedSize() is an estimate

isSizeEstimate() - Method in interface org.intermine.api.results.WebTable

Check whether the result of getEstimatedSize() is an estimate

isSizeEstimate() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Check whether the result of getSize is an estimate

isStored - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

ISSUE_KEYS - Static variable in class org.intermine.api.bag.BagQueryResult

keys of the map in a set

issueToken(Profile, int) - Method in class org.intermine.webservice.server.JWTBuilder

Issue a new token for the given profile.

IssueTokenTask - Class in org.intermine.web.task

A task that will issue a signed JWT token for the current configuration.

IssueTokenTask() - Constructor for class org.intermine.web.task.IssueTokenTask

isSummarised(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser

Returns true if the given template has been summarised.

isSuperUser - Variable in class org.intermine.api.profile.Profile

isSuperuser() - Method in class org.intermine.api.profile.Profile

Return true if and only if the user logged is superuser

isSuperuser() - Method in class org.intermine.api.util.AnonProfile

isSuperUser(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Return true if and only if the current user if the superuser.

isToUpgrade() - Method in class org.intermine.api.profile.InterMineBag

Return true if the status bag is to_upgrade, otherwise false

isTransitive() - Method in class org.intermine.bio.ontology.OboTypeDefinition

isTreatColNames() - Method in class org.intermine.web.tags.table.TableTag

isTrue(Map<?, ?>, String) - Static method in class org.intermine.bio.ontology.OboParser

Given the tag+value map for a term, return whether it's true or false

isTruncated(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if a query using the given table-mastering ClassDescriptor would require a constraint on the className field.

isUncompressed() - Method in class org.intermine.webservice.server.WebService

isUniquelyMappedEnsemblId(String, String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser

Return true if the given Ensembl identifier is assigned to only one gene for the taxon specified.

isUniqueSymbol(String, String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser

Return true if the given symbol is is assigned to only one gene for the taxon specified.

isUpdated - Variable in class org.intermine.api.profile.PathQueryUpdate

isUpdated() - Method in class org.intermine.api.profile.PathQueryUpdate

Return true if the pathquery has been updated

isValid(String, String, String, UserProfile) - Method in interface org.intermine.api.profile.TagChecker

Returns true if and only the given arguments are valid fields for a tag of this type.

isValid() - Method in class org.intermine.pathquery.PathQuery

Returns true if the query verifies correctly.

isValidEditableConstraintType() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint

Return true if this type of constraint can be set as editable in a template query - i.e. if it is an attribute or lookup constraint or null constraint.

isValidName(String) - Static method in class org.intermine.api.util.NameUtil

Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.

isValidName(String, boolean) - Static method in class org.intermine.api.util.NameUtil

Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.

isValidRange() - Method in class org.intermine.web.logic.query.DisplayConstraint

isValidTagName(String) - Static method in class org.intermine.api.profile.TagManager

TODO this should use the same validation method the other classes use Verifies that tag name can only contain A-Z, a-z, 0-9, '_', '-', ' ', ':', '.'

isValidValue(String) - Method in class org.intermine.bio.chado.config.MatchingFieldConfigAction

Validate a value for this field by matching with pattern set in the constructor.

isValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint

Return true if editing an existing constraint and an attribute value or LOOKUP constraint was selected.

isVerbose() - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Returns true if the optimiser will print out stuff.

isVersionAtLeast(String) - Method in class org.intermine.sql.Database

Return true if the database version is at least as high as the test number given, taking into account major and minor versions. e.g. test if database is at least 9.2

isVisible() - Method in class org.intermine.api.results.Column

Gets the value of visible

isWindowsClient(HttpServletRequest) - Static method in class org.intermine.web.logic.RequestUtil

isWithinLimit(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory

Check that this requester is within their limit.

isZip() - Method in class org.intermine.webservice.server.WebService

Item - Class in org.intermine.webservice.client.results

A representation of an individual result from the web-services.

Item(ServiceFactory, String, Map<String, Object>) - Constructor for class org.intermine.webservice.client.results.Item

Construct an Item.

Item - Class in org.intermine.xml.full

Representation of an object

Item() - Constructor for class org.intermine.xml.full.Item

Construct an item.

Item(Model, String, String, String) - Constructor for class org.intermine.xml.full.Item

Construct an item.

Item(String, String, String) - Constructor for class org.intermine.xml.full.Item

Construct an item with no Model.

ItemFactory - Class in org.intermine.xml.full

ItemFactory class

ItemFactory() - Constructor for class org.intermine.xml.full.ItemFactory

Create an ItemFactory that isn't specific to a particular model.

ItemFactory(Model) - Constructor for class org.intermine.xml.full.ItemFactory

Create an ItemFactory specific to a particular model.

ItemFactory(Model, String) - Constructor for class org.intermine.xml.full.ItemFactory

Create an ItemFactory specific to a particular model.

ItemHelper - Class in org.intermine.xml.full

Class providing Item utility methods

ItemList - Class in org.intermine.webservice.client.lists

A representation of a list of objects stored on the server.

items - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

ItemToObjectTranslator - Class in org.intermine.dataconversion

Translator that translates fulldata Items to business objects

ItemToObjectTranslator(Model, ObjectStore) - Constructor for class org.intermine.dataconversion.ItemToObjectTranslator

Constructor

ItemWriter - Interface in org.intermine.dataconversion

Stores Items in something - an objectstore or otherwise.

iter - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

iterator() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

iterator() - Method in class org.intermine.api.results.WebResults

iterator() - Method in class org.intermine.api.search.SearchResults

iterator() - Method in class org.intermine.objectstore.proxy.ProxyCollection

iterator() - Method in class org.intermine.objectstore.query.Results

iterator() - Method in class org.intermine.util.ConsistentSet

Return an iterator for the elements in the Set.

iterator() - Method in class org.intermine.util.IteratorIterable

Returns the iterator.

iterator() - Method in class org.intermine.util.PseudoSet

iterator - Variable in class org.intermine.util.SynchronisedIterator

iterator() - Method in class org.intermine.webservice.client.lists.ItemList

iterator() - Method in class org.intermine.webservice.client.results.ResultRowList

iterator() - Method in class org.intermine.webservice.server.core.TableRowIterator

iteratorFrom(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

iteratorFrom(int) - Method in class org.intermine.api.results.WebResults

iteratorFrom(int) - Method in class org.intermine.objectstore.query.Results

Returns an iterator over the List, starting from the given position.

IteratorIterable<T> - Class in org.intermine.util

This is an Iterable that returns a given Iterator.

IteratorIterable(Iterator<T>) - Constructor for class org.intermine.util.IteratorIterable

Constructs an Iterable from an Iterator.

iteratorIterator - Variable in class org.intermine.util.CombinedIterator

J

JavaModelOutput - Class in org.intermine.codegen

Maps InterMine metadata to Java source files

JavaModelOutput(Model, File) - Constructor for class org.intermine.codegen.JavaModelOutput

Constructor.

javaNameToSO(String) - Static method in class org.intermine.bio.util.BioConverterUtil

Get SO name for Java class, eg.

Job - Interface in org.intermine.api.idresolution

Job.JobStatus - Enum in org.intermine.api.idresolution

JobInput - Interface in org.intermine.api.idresolution

JobJanitor - Class in org.intermine.webservice.server.idresolution

Wake up once a minute and evict old completed jobs.

JobJanitor() - Constructor for class org.intermine.webservice.server.idresolution.JobJanitor

JobRemovalService - Class in org.intermine.webservice.server.idresolution

JobRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.JobRemovalService

JobResultsService - Class in org.intermine.webservice.server.idresolution

JobResultsService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobResultsService

Construct a jobs service handler.

JobStatusService - Class in org.intermine.webservice.server.idresolution

JobStatusService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobStatusService

Construct a handler for this request.

joinType - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

JSON_FORMATS - Static variable in enum org.intermine.webservice.server.Format

The JSON formats: JSON, OBJECTS, TABLE, ROWS

JSONCountFormatter - Class in org.intermine.webservice.server.output

A formatter that presents count results as JSON.

JSONCountFormatter() - Constructor for class org.intermine.webservice.server.output.JSONCountFormatter

JSONDataTableRowIterator - Class in org.intermine.webservice.server.output

JSONDataTableRowIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowIterator

Constructor

JSONDataTableRowResultProcessor - Class in org.intermine.webservice.server.output

A result processor for result rows.

JSONDataTableRowResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor

Constructor.

JSONFormatter - Class in org.intermine.webservice.server.output

Base class for formatters that process JSON data.

JSONFormatter() - Constructor for class org.intermine.webservice.server.output.JSONFormatter

Constructor

JSONFormattingException - Exception in org.intermine.webservice.server.output

JSONFormattingException(String) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException

JSONFormattingException(String, Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException

JSONFormattingException(Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException

JSONListFormatter - Class in org.intermine.webservice.server.lists

JSONListFormatter(InterMineAPI, Profile, boolean) - Constructor for class org.intermine.webservice.server.lists.JSONListFormatter

Construct a list formatter.

JSONObjectFormatter - Class in org.intermine.webservice.server.output

JSONObjectFormatter() - Constructor for class org.intermine.webservice.server.output.JSONObjectFormatter

Constructor

JSONObjResultProcessor - Class in org.intermine.webservice.server.output

JSONObjResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONObjResultProcessor

Constructor.

JSONResult - Class in org.intermine.webservice.client.results

JSONResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.JSONResult

Constructor

JSONResult(String) - Constructor for class org.intermine.webservice.client.results.JSONResult

Constructor with a string

JSONResultFormatter - Class in org.intermine.webservice.server.output

JSONResultFormatter() - Constructor for class org.intermine.webservice.server.output.JSONResultFormatter

JSONResultProcessor - Class in org.intermine.webservice.server.output

An class that defines the basic methods for processing JSON results.

JSONResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONResultProcessor

Constructor.

JSONResultsIterator - Class in org.intermine.webservice.server.output

A class to to produce a sequence of JSONObjects from a set of database rows.

JSONResultsIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONResultsIterator

Constructor.

JsonRow - Class in org.intermine.webservice.client.results

Class representing a row of data as a list.

JsonRow(JSONArray) - Constructor for class org.intermine.webservice.client.results.JsonRow

Construct a new result row object backed by the given JSONArray.

JsonRow(String) - Constructor for class org.intermine.webservice.client.results.JsonRow

Construct a new result row object backed by the JSONArray which can be parsed from the given String.

JSONRowFormatter - Class in org.intermine.webservice.server.output

JSONRowFormatter() - Constructor for class org.intermine.webservice.server.output.JSONRowFormatter

Constructor

JSONRowIterator - Class in org.intermine.webservice.server.output

JSONRowIterator(ExportResultsIterator, InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowIterator

Constructor

JsonRowMap - Class in org.intermine.webservice.client.results

Class representing a row of data as a map.

JsonRowMap(JSONArray, List<String>) - Constructor for class org.intermine.webservice.client.results.JsonRowMap

Construct a result-row with a JSONArray as its backing data store.

JsonRowMap(String, List<String>) - Constructor for class org.intermine.webservice.client.results.JsonRowMap

Construct a result-row with a String as its backing data store.

JSONRowResultProcessor - Class in org.intermine.webservice.server.output

A result processor for result rows.

JSONRowResultProcessor(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor

Constructor.

JSONRowResultProcessor(InterMineAPI, JSONRowResultProcessor.Verbosity) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor

Construct a row result processor.

JSONRowResultProcessor.Verbosity - Enum in org.intermine.webservice.server.output

JSONService - Class in org.intermine.webservice.server.core

A Service that has specialisations for supplying JSON.

JSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.JSONService

Constructor

JSONSummaryProcessor - Class in org.intermine.webservice.server.output

A processor for summary results in JSON format.

JSONSummaryProcessor() - Constructor for class org.intermine.webservice.server.output.JSONSummaryProcessor

JSONTableFormatter - Class in org.intermine.webservice.server.output

JSONTableFormatter() - Constructor for class org.intermine.webservice.server.output.JSONTableFormatter

Constructor.

JSONTableResultProcessor - Class in org.intermine.webservice.server.output

JSONTableResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONTableResultProcessor

Constructor.

JSONWidgetProcessor - Class in org.intermine.webservice.server.widget

JSStrings - Class in org.intermine.api.query.codegen

JWTBuilder - Class in org.intermine.webservice.server

A class that encapsulates the logic required to generate JWT tokens for users.

JWTBuilder(PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder

Constructor

JWTBuilder(JWTBuilder.Algorithm, PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder

Constructor

JWTBuilder.Algorithm - Enum in org.intermine.webservice.server

The signing algorithms this builder supports.

JWTVerifier - Class in org.intermine.webservice.server

A class to encapsulate the logic for verifying identity claims as represented as JWTs (JSON Web Tokens).

JWTVerifier(PublicKeySource, Properties) - Constructor for class org.intermine.webservice.server.JWTVerifier

Construct a verifier.

JWTVerifier.Verification - Class in org.intermine.webservice.server

The result of a successful verification.

JWTVerifier.VerificationError - Exception in org.intermine.webservice.server

An error that declares that something has gone wrong when trying to verify a JWT.

JWTVerifier.VerificationError(String) - Constructor for exception org.intermine.webservice.server.JWTVerifier.VerificationError

Initialise a new verification error with a message detailing the problem.

K

KeggPathwayConverter - Class in org.intermine.bio.dataconversion

DataConverter to load Kegg Pathways and link them to Genes

KeggPathwayConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.KeggPathwayConverter

Constructor

KEY_CALLBACK - Static variable in class org.intermine.webservice.server.output.JSONFormatter

The key for the callback

KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.HTMLTableFormatter

The key for setting headers

KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the title.

KEY_COUNT - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the count.

KEY_CURRENT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attribute for the current page

KEY_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager

Name of the key under which to store the serialized version of the key definitions

KEY_DESCRIPTION - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the description.

KEY_EXPORT_CSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the CSV export URL.

KEY_EXPORT_TSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the TSV export URL.

KEY_HEADER_OBJS - Static variable in class org.intermine.webservice.server.output.JSONFormatter

Things that should go into the header

KEY_INTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter

the key for the result object.

KEY_KV_PAIRS - Static variable in class org.intermine.webservice.server.output.JSONFormatter

A map of optional key value pairs that should go in the header of the object.

KEY_MODEL_NAME - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter

The key for the model name

KEY_NEXT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the next page

KEY_OUTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter

The way to wrap up after the result.

KEY_PREVIOUS_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the previous page

KEY_QUOTE - Static variable in class org.intermine.webservice.server.output.JSONFormatter

Whether we should quote the result item.

KEY_ROOT_CLASS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter

The key for the root class

KEY_TIME - Static variable in class org.intermine.webservice.server.output.JSONFormatter

The key for the execution time

KEY_TITLE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter

The key for setting the header attributes for the title.

KEY_VIEWS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter

The key for the views

KeyDecoder - Interface in org.intermine.web.security

Classes that can decode public keys from strings.

keyField - Variable in class org.intermine.api.results.ResultElement

KeyFormatException - Exception in org.intermine.api.query

KeyFormatException(String, NumberFormatException) - Constructor for exception org.intermine.api.query.KeyFormatException

KEYLESS_CLASSES_MAP - Static variable in class org.intermine.web.logic.Constants

Key for a Map from class name to Boolean.TRUE for all classes in the model that do not have any class keys.

KeySearchTrack - Class in org.intermine.api.tracker.track

KeySearchTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.KeySearchTrack

KeySearchTracker - Class in org.intermine.api.tracker

KeySearchTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.KeySearchTracker

Build a search tracker

keySet() - Method in class org.intermine.util.AlwaysMap

keySet() - Method in class org.intermine.util.IdentityMap

keySet() - Method in class org.intermine.util.ReferenceMap

KeySigner - Class in org.intermine.web.security

Issue certificates for keys we trust.

KeySigner(PrivateKey, String, int, String) - Constructor for class org.intermine.web.security.KeySigner

Build a new signer.

KeySigner.SigningException - Exception in org.intermine.web.security

Errors thrown when signing certificates.

KeySourceException - Exception in org.intermine.web.security

Errors encountered when using a PublicKeySource

KeySourceException(Throwable) - Constructor for exception org.intermine.web.security.KeySourceException

An error caused by another error

KeyStoreBuilder - Class in org.intermine.web.security

Build a key store from some options and possibly a keystore file.

KeyStoreBuilder(Properties, ResourceOpener) - Constructor for class org.intermine.web.security.KeyStoreBuilder

Construct a new KeyStoreBuilder.

KeyStorePublicKeySource - Class in org.intermine.web.security

A public key store that reads keys from a key store.

KeyStorePublicKeySource(KeyStore) - Constructor for class org.intermine.web.security.KeyStorePublicKeySource

Build a key source that reads them from a key store.

KeyStoreTask - Class in org.intermine.web.task

Base task for tasks that require a key store.

KeyStoreTask() - Constructor for class org.intermine.web.task.KeyStoreTask

KeywordSearch - Class in org.intermine.api.lucene

Allows for full-text searches over all metadata using the apache lucene engine.

KeywordSearchFacet - Class in org.intermine.api.lucene

container for one faceting field, the current faceting value and the list of possible items

KeywordSearchFacet(String, String, String, List<BrowseFacet>) - Constructor for class org.intermine.api.lucene.KeywordSearchFacet

constructor

KeywordSearchFacetData - Class in org.intermine.api.lucene

container class for a facet field and its settings

KeywordSearchFacetData(String, String, KeywordSearchFacetType) - Constructor for class org.intermine.api.lucene.KeywordSearchFacetData

convenience constructor for single field

KeywordSearchFacetData(String[], String, KeywordSearchFacetType) - Constructor for class org.intermine.api.lucene.KeywordSearchFacetData

constructor

KeywordSearchFacetType - Enum in org.intermine.api.lucene

type of faceting to use see http://snaprojects.jira.com/wiki/display/BOBO/Create+a+Browse+Index

KeywordSearchHit - Class in org.intermine.api.lucene

container class to hold a document found in an keyword search together with its object and score

KeywordSearchHit(float, Document, InterMineObject) - Constructor for class org.intermine.api.lucene.KeywordSearchHit

constructor

KeywordSearchResult - Class in org.intermine.web.search

Container for a single result row from the keyword search

KeywordSearchResult(WebConfig, InterMineObject, Map<String, List<FieldDescriptor>>, ClassDescriptor, float, Map<String, TemplateQuery>, String) - Constructor for class org.intermine.web.search.KeywordSearchResult

create the container object - automatically reads fields and saves the results in members

KeywordSearchResultsController - Class in org.intermine.web.struts

Controller for keyword search.

KeywordSearchResultsController() - Constructor for class org.intermine.web.struts.KeywordSearchResultsController

L

LabelsSummaryAction - Class in org.intermine.web.struts

An action that presents how all the labels configured for classes and their top-level fields appear.

LabelsSummaryAction() - Constructor for class org.intermine.web.struts.LabelsSummaryAction

labourer - Variable in class org.intermine.webservice.server.output.FlatFileFormatter

last(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Change to the last results page

last(int) - Method in class org.intermine.webservice.client.results.Page

Get the last page.

lastBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

lastGet - Variable in class org.intermine.objectstore.query.Results

lastIndexOf(Object) - Method in class org.intermine.webservice.client.results.ResultRowList

lastPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Go to the last page

lastSource - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

lastTickle - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout

Time of last call to tickle.

LAYOUT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser

Layout parameter name.

Lazy - Interface in org.intermine.objectstore.proxy

Class which uses an ObjectStore to perform lazy fetching of data

LazyCollection<E> - Interface in org.intermine.objectstore.proxy

Class which uses an ObjectStore to perform lazy fetching of data

lazyList() - Method in class org.intermine.webservice.server.core.JSONService

lazyList() - Method in class org.intermine.webservice.server.data.DataService

LEAF_DESCRIPTORS_MAP - Static variable in class org.intermine.web.logic.Constants

Servlet attribute.

LEAST - Static variable in class org.intermine.objectstore.query.QueryExpression

Return the lowest value from two expressions, e.g.

LEAST - Static variable in class org.intermine.sql.query.Function

LEAST(x, y) - takes two operands

left - Variable in class org.intermine.objectstore.query.OverlapConstraint

left - Variable in class org.intermine.sql.query.Constraint

left - Variable in class org.intermine.sql.query.InListConstraint

left - Variable in class org.intermine.sql.query.SubQueryConstraint

LEFT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

LEFT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the left is always false.

LEFT_FALSE_RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the left is always false, and the right is always true.

LEFT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the left is always true.

LEFT_TRUE_RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the left is always true, and the right is always false.

length - Variable in class org.intermine.objectstore.query.ClobAccess

length() - Method in class org.intermine.objectstore.query.ClobAccess

Returns the length of this character sequence.

length() - Method in class org.intermine.objectstore.query.PendingClob

Returns the length of this character sequence.

LESS - Static variable in class org.intermine.sql.query.AbstractValue

Describes one AbstractValue as being less than another AbstractValue.

lessOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare the value of this AbstractValue with another to see if it is less or equal.

lessThan(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be less than a value.

lessThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare the value of this AbstractValue with another to see if it is less.

lessThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be less than or equal to a value.

like(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be LIKE a value.

LIKE - Static variable in class org.intermine.sql.query.Constraint

An operation for this constraint indicating that left should be pattern-matched against right.

limit - Variable in class org.intermine.sql.query.Query

LIMIT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Name of size parameter that determines number of returned results.

limitedContext - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

LimitedMap<K,V> - Class in org.intermine.api.util

A caching map that drops its eldest entries if the map grows beyond a certain size.

LimitedMap(int) - Constructor for class org.intermine.api.util.LimitedMap

LimitOffsetQuery - Class in org.intermine.sql.precompute

A class specifically for use with the OptimiserCache, designed to split a SQL string into its functional part, and the limit and offset.

LimitOffsetQuery(String) - Constructor for class org.intermine.sql.precompute.LimitOffsetQuery

Creates a new LimitOffsetQuery object from this query string.

linkedHashMapAdd(LinkedHashMap<K, V>, K, K, V) - Static method in class org.intermine.util.CollectionUtil

Return a copy of the given map with the object inserted at the given index.

linkFile - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

LinkGeneratorBase - Class in org.intermine.webservice.server

Base class for link generators.

LinkGeneratorBase() - Constructor for class org.intermine.webservice.server.LinkGeneratorBase

Empty constructor.

LinkRedirectManager - Class in org.intermine.api

Class to manage external links.

LinkRedirectManager(Properties) - Constructor for class org.intermine.api.LinkRedirectManager

Constructor

linkRedirector - Variable in class org.intermine.api.InterMineAPI

list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction

Load a query using given list

list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction

Load a template from template name passed as parameter.

LIST_NAME_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService

LIST_SEPARATOR - Static variable in class org.intermine.webservice.server.lists.ListInput

The separator used between lists when passed joined together.

LIST_SIZE_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService

LIST_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of class that tracks lists

LIST_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of table that tracks lists

ListAppendService - Class in org.intermine.webservice.server.lists

ListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListAppendService

ListBuildMode - Enum in org.intermine.api.tracker.util

ListCreationInput - Class in org.intermine.webservice.server.lists

Class representing the input to a list creation request.

ListCreationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListCreationInput

Constructor.

ListDeletionService - Class in org.intermine.webservice.server.lists

A service for deleting lists from the user-profile database.

ListDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDeletionService

Constructor.

ListDifferenceService - Class in org.intermine.webservice.server.lists

A service for performing a symmetric difference operation on a collection of lists.

ListDifferenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDifferenceService

Constructor

ListFormatter - Interface in org.intermine.webservice.server.lists

The common interface for formatters that know how to format lists.

ListFunctions - Class in org.intermine.webservice.server.core

Similar to Apache CollectionUtils - but with Generics.

ListInput - Class in org.intermine.webservice.server.lists

Class representing input to a list service request.

ListInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListInput

Parse the values from the request, and validate them.

ListIntersectionService - Class in org.intermine.webservice.server.lists

A service that intersects one or more lists.

ListIntersectionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListIntersectionService

listIterator() - Method in class org.intermine.webservice.client.results.ResultRowList

listIterator(int) - Method in class org.intermine.webservice.client.results.ResultRowList

listLeft - Variable in class org.intermine.web.struts.ModifyBagForm

ListMaker<T> - Interface in org.intermine.webservice.server.lists

The type of things that can make lists.

ListMakerService - Class in org.intermine.webservice.server.lists

A base class for all list services that create lists.

ListMakerService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListMakerService

Constructor.

ListManager - Class in org.intermine.webservice.server.core

Manager of public lists used by web service.

ListManager(InterMineAPI, Profile) - Constructor for class org.intermine.webservice.server.core.ListManager

ListManager constructor.

ListOperationService - Class in org.intermine.webservice.server.lists

A base class for services that perform operations on lists.

ListOperationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListOperationService

Constructor.

listRelatedConstraints(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Return a List of Constraint objects that relate to the given FromElement.

ListRenameInput - Class in org.intermine.webservice.server.lists

Class for encapsulating the input to a list rename request.

ListRenameInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListRenameInput

Constructor.

ListRenameService - Class in org.intermine.webservice.server.lists

A service for renaming lists.

ListRenameService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListRenameService

Constructor.

ListRenameServlet - Class in org.intermine.webservice.server.lists

ListRenameServlet() - Constructor for class org.intermine.webservice.server.lists.ListRenameServlet

listRight - Variable in class org.intermine.web.struts.ModifyBagForm

Lists - Class in org.intermine.webservice.client.lists

Utilities for parsing lists from their JSON representation.

LISTS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

The lists to operate on

listsButton - Variable in class org.intermine.web.struts.ModifyBagForm

ListService - Class in org.intermine.webservice.client.services

An interface to all the resources that represent list information and list operations available at an InterMine implementation.

ListService(String, String) - Constructor for class org.intermine.webservice.client.services.ListService

Use ServiceFactory instead of constructor for creating this service .

ListService.ListCreationInfo - Class in org.intermine.webservice.client.services

An abstraction of the combination of options that can be specified to generate a new list in a list creation operation.

ListService.ListCreationInfo(String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle with all possible optional values set to their defaults.

ListService.ListCreationInfo(PathQuery) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, specifying the query to use to find objects with.

ListService.ListCreationInfo(PathQuery, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, specifying the name.

ListService.ListCreationInfo(String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, with the name taken from the supplied value.

ListService.ListCreationInfo(PathQuery, String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, specifying the name and the description.

ListService.ListCreationInfo(String, String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, with the name and description taken from the supplied value.

ListService.ListCreationInfo(PathQuery, String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, specifying all parameters.

ListService.ListCreationInfo(String, String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo

Create a new options bundle, specifying all parameters.

ListService.ListOperationInfo - Class in org.intermine.webservice.client.services

An abstraction of the combination of options that can be specified to generate a new list in a list operation.

ListService.ListOperationInfo() - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo

Create a new options bundle with all values set to their defaults.

ListService.ListOperationInfo(String) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo

Create a new options bundle, with all elements set to their default apart from the name, which is given.

ListService.ListOperationInfo(String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo

Create a new options bundle, with all elements set to their default apart from the name and the description, which are given.

ListService.ListOperationInfo(String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo

Create a new options bundle, specifying all options.

ListServiceUtils - Class in org.intermine.webservice.server.lists

Utility functions for dealing with list requests.

ListShareCreationService - Class in org.intermine.webservice.server.lists

ListShareCreationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareCreationService

ListShareDeletionService - Class in org.intermine.webservice.server.lists

ListShareDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDeletionService

ListShareDetailsService - Class in org.intermine.webservice.server.lists

ListShareDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDetailsService

ListShareServlet - Class in org.intermine.webservice.server.lists

ListShareServlet() - Constructor for class org.intermine.webservice.server.lists.ListShareServlet

ListSharingInvitationAcceptanceService - Class in org.intermine.webservice.server.lists

ListSharingInvitationAcceptanceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService

ListSharingInvitationDeletionService - Class in org.intermine.webservice.server.lists

ListSharingInvitationDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService

Construct a service handler.

ListSharingInvitationDetailsService - Class in org.intermine.webservice.server.lists

ListSharingInvitationDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService

ListSharingInvitationService - Class in org.intermine.webservice.server.lists

Invite a user to share a list.

ListSharingInvitationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationService

ListSharingInvitationServlet - Class in org.intermine.webservice.server.lists

ListSharingInvitationServlet() - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationServlet

ListsRequestParser - Class in org.intermine.webservice.server.lists

Request processor for ListsService that process request, validates it and returns parsed input as a parameter object.

ListsRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.lists.ListsRequestParser

ListsRequestProcessor constructor.

ListsService - Class in org.intermine.webservice.server.lists

Web service that returns all public lists (bags) that contain object with specified id.

ListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListsService

Constructor

ListsServiceInput - Class in org.intermine.webservice.server.lists

ListsServiceInput is parameter object representing parameters for ListService web service.

ListsServiceInput() - Constructor for class org.intermine.webservice.server.lists.ListsServiceInput

ListSubtractionService - Class in org.intermine.webservice.server.lists

A service for subtracting one group of lists from another group of lists to produce a new list.

ListSubtractionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSubtractionService

Constructor

ListTagAddingService - Class in org.intermine.webservice.server.lists

A service for adding tags to a list.

ListTagAddingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagAddingService

Constructor.

ListTagRemovalService - Class in org.intermine.webservice.server.lists

A service for removing tags from a list.

ListTagRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagRemovalService

Constructor.

ListTagService - Class in org.intermine.webservice.server.lists

A service for getting the tags of a list.

ListTagService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagService

Constructor.

ListTrack - Class in org.intermine.api.tracker.track

Class to represent the track for the lists objects.

ListTrack(String, int, ListBuildMode, ListTrackerEvent, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.ListTrack

ListTrack(String, int, ListBuildMode, ListTrackerEvent) - Constructor for class org.intermine.api.tracker.track.ListTrack

LISTTRACK - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding

label for XML

ListTrackBinding - Class in org.intermine.api.tracker.xml

ListTracker - Class in org.intermine.api.tracker

ListTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.ListTracker

Build a list tracker

ListTrackerEvent - Enum in org.intermine.api.tracker.util

LISTTRACKS - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding

label for XML

ListUnionService - Class in org.intermine.webservice.server.lists

A class for exposing creating unions of lists as a resource.

ListUnionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUnionService

Constructor.

ListUploadService - Class in org.intermine.webservice.server.lists

A class to create a new list with via a set of identifiers uploaded by a user.

ListUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUploadService

Constructor

load(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction

Load a query.

LoadBagValuesTask - Class in org.intermine.web.task

Task to load bagvalues table in the userprofile database.

LoadBagValuesTask() - Constructor for class org.intermine.web.task.LoadBagValuesTask

loadClassKeyDefinitions() - Static method in class org.intermine.modelproduction.MetadataManager

Load the class key / key field definitions.

LoadDefaultTemplatesTask - Class in org.intermine.web.task

Load template queries form an XML file into a given user profile.

LoadDefaultTemplatesTask() - Constructor for class org.intermine.web.task.LoadDefaultTemplatesTask

loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper

loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper.RangeConfig

LOADING - Static variable in class org.intermine.objectstore.query.PrefetchManager

loadKeyDefinitions(String) - Static method in class org.intermine.modelproduction.MetadataManager

Load the key definitions file for the named model from the classpath

loadProperties(String) - Static method in class org.intermine.util.PropertiesUtil

Load a specified properties file

loadQuery(PathQuery, HttpSession, HttpServletResponse) - Static method in class org.intermine.web.logic.session.SessionMethods

Load a query into the session, cloning to avoid modifying the original

LoadQueryAction - Class in org.intermine.web.struts

Implementation of Action that sets the current Query for the session from some random XML the user has passed in, and maybe executes it.

LoadQueryAction() - Constructor for class org.intermine.web.struts.LoadQueryAction

LoadTemplateAction - Class in org.intermine.web.struts

Implementation of Action that runs a template

LoadTemplateAction() - Constructor for class org.intermine.web.struts.LoadTemplateAction

LocalMine - Class in org.intermine.api.mines

A mine that refers to the local application instance.

LocalMine(InterMineAPI, Properties) - Constructor for class org.intermine.api.mines.LocalMine

Construct a mine that refers to the local application instance.

lock - Static variable in class org.intermine.sql.logging.QueryLogger

locusTag - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

LOG - Static variable in class org.intermine.api.bag.operations.BagOperation

LOG - Static variable in class org.intermine.api.profile.InterMineBag

LOG - Static variable in class org.intermine.api.profile.InvalidBag

LOG - Static variable in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

LOG - Static variable in class org.intermine.api.results.WebResults

LOG - Static variable in class org.intermine.bio.dataconversion.ChadoDBConverter

LOG - Static variable in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

LOG - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

LOG - Static variable in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.HgncIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.HumanIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.IdResolverService

LOG - Static variable in class org.intermine.bio.dataconversion.KeggPathwayConverter

LOG - Static variable in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.NcbiGeneInfoParser

LOG - Static variable in class org.intermine.bio.dataconversion.OntologyIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.PubMedGeneConverter

LOG - Static variable in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

LOG - Static variable in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory

LOG - Static variable in class org.intermine.bio.task.GFF3ConverterTask

LOG - Static variable in class org.intermine.bio.util.BioUtil

LOG - Static variable in class org.intermine.dwr.AjaxServices

LOG - Static variable in class org.intermine.dwr.TrackAjaxServices

log - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

LOG - Static variable in class org.intermine.pathquery.Path

log(Query, Writer) - Static method in class org.intermine.sql.logging.QueryLogger

Allows a Query to be logged

LOG - Static variable in class org.intermine.task.DynamicAttributeTask

LOG - Static variable in class org.intermine.task.FileConverterTask

LOG - Static variable in class org.intermine.web.displayer.DisplayerManager

LOG - Static variable in class org.intermine.web.logic.export.http.StandardHttpExporter

LOG - Static variable in class org.intermine.web.logic.export.ResultElementConverter

LOG - Static variable in class org.intermine.web.logic.results.DisplayField

LOG - Static variable in class org.intermine.web.logic.results.InlineResultsTable

LOG - Static variable in class org.intermine.web.logic.session.SessionMethods

LOG - Static variable in class org.intermine.web.logic.WebUtil

LOG - Static variable in class org.intermine.web.struts.ContactAction

LOG - Static variable in class org.intermine.web.struts.CreateTemplateAction

LOG - Static variable in class org.intermine.web.struts.ExportQueryAction

LOG - Static variable in class org.intermine.web.struts.HtmlHeadController

LOG - Static variable in class org.intermine.web.struts.InterMineExceptionHandler

LOG - Static variable in class org.intermine.web.struts.ObjectTrailController

LOG - Static variable in class org.intermine.web.struts.ObjectViewController

LOG - Static variable in class org.intermine.web.struts.PollQueryAction

LOG - Static variable in class org.intermine.web.struts.QueryBuilderChange

LOG - Static variable in class org.intermine.web.struts.QueryBuilderController

LOG - Static variable in class org.intermine.web.struts.RequestPasswordAction

LOG - Static variable in class org.intermine.web.struts.SaveBagAction

LOG - Static variable in class org.intermine.web.struts.SaveFromIdsToBagAction

LOG - Static variable in class org.intermine.web.struts.SaveQueryAction

LOG - Static variable in class org.intermine.web.struts.SummariseTemplatesAction

LOG - Static variable in class org.intermine.web.struts.TableExportAction

LOG - Static variable in class org.intermine.web.struts.TemplatesExportAction

LOG - Static variable in class org.intermine.web.struts.WebserviceCodeGenAction

LOG - Static variable in class org.intermine.webservice.server.query.CodeService

logBeforeExecute - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

logError(String) - Method in class org.intermine.web.task.KeyStoreTask

Log a message to standard error.

logEverything - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

logExampleQueryUse(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods

Log load of an example query.

logExplains - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

LogicExpression - Class in org.intermine.pathquery

In memory representation of constraint logic expression.

LogicExpression(String) - Constructor for class org.intermine.pathquery.LogicExpression

Create a new instance of LogicExpression parsing the given expression.

LogicExpression.And - Class in org.intermine.pathquery

An AND operator node.

LogicExpression.Node - Class in org.intermine.pathquery

Node of parse tree.

LogicExpression.Node() - Constructor for class org.intermine.pathquery.LogicExpression.Node

LogicExpression.Operator - Class in org.intermine.pathquery

An operator node.

LogicExpression.Or - Class in org.intermine.pathquery

An OR operator node.

LogicExpression.Variable - Class in org.intermine.pathquery

A variable node.

LOGIN_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of class that tracks lists

LOGIN_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of table that tracks logins

LoginAction - Class in org.intermine.web.struts

Action to handle button presses on the main tile

LoginAction() - Constructor for class org.intermine.web.struts.LoginAction

LoginController - Class in org.intermine.web.struts

Controller for the login page.

LoginController() - Constructor for class org.intermine.web.struts.LoginController

LoginForm - Class in org.intermine.web.struts

The main form, using for editing constraints

LoginForm() - Constructor for class org.intermine.web.struts.LoginForm

LoginHandler - Class in org.intermine.web.logic.profile

LoginHandler() - Constructor for class org.intermine.web.logic.profile.LoginHandler

LoginTrack - Class in org.intermine.api.tracker.track

LoginTrack(String, Timestamp) - Constructor for class org.intermine.api.tracker.track.LoginTrack

LOGINTRACK - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding

label for XML

LoginTrackBinding - Class in org.intermine.api.tracker.xml

LoginTracker - Class in org.intermine.api.tracker

Class for tracking when the users log into their accounts.

LoginTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.LoginTracker

Build a login tracker

LOGINTRACKS - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding

label for XML

logMessage(String) - Method in class org.intermine.web.task.KeyStoreTask

Log a message to standard out.

LogoutAction - Class in org.intermine.web.struts

Action that invalidates the user session effectively logging the user out of intermine.

LogoutAction() - Constructor for class org.intermine.web.struts.LogoutAction

logQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Before running a query via web services, add to query history and add a track

logTableBatch - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

logTableConnection - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

logTableName - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

logTemplateQueryUse(HttpSession, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods

Log use of a template query.

lookup(String, String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path with the LOOKUP operator.

lookup(String, int) - Method in class org.intermine.sql.precompute.OptimiserCache

Attempts to find a match in the cache for an original query.

LOOKUP_CONSTRAINT - Static variable in class org.intermine.api.config.Constants

LOOKUP constraint

LOOKUP_MSG - Static variable in class org.intermine.web.logic.Constants

Session attribute that holds message when a lookup constraint has been used

lookupCategory(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Returns a Map from original SQL to PrecomputedTable for a given category in the manager.

lookupOs - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

lookupSql(String, String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Returns a PrecomputedTable object if one exists in the manager with the given category and original SQL string.

lookupSql(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Returns a PrecomputedTable object if one exists in the manager with the given original SQL string.

LookupTokeniser - Class in org.intermine.api.query

Class for tokenising identifier input.

LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

loopQueryOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

loopQueryValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

LOWER - Static variable in class org.intermine.objectstore.query.QueryExpression

Lower case version of the given string

LOWER - Static variable in class org.intermine.sql.query.Function

LOWER operator - takes one operand

LT - Static variable in class org.intermine.sql.query.Constraint

An operation for this constraint indicating that left is less than right.

LuceneIndex - Class in org.intermine.web.autocompletion

Creates the indexes for LuceneObjectClasses

LuceneIndex(String) - Constructor for class org.intermine.web.autocompletion.LuceneIndex

Constructor

LuceneObjectClass - Class in org.intermine.web.autocompletion

LuceneObjectClass contains data for the autocompletion

LuceneObjectClass(String) - Constructor for class org.intermine.web.autocompletion.LuceneObjectClass

Constructor

LuceneSearchEngine - Class in org.intermine.web.autocompletion

LuceneSearchEngine for the autocompleter

LuceneSearchEngine(String) - Constructor for class org.intermine.web.autocompletion.LuceneSearchEngine

LuceneSearchEngine constructor put the indexes to memory and creates an keyword analyser

LuceneSearchEngine(RAMDirectory) - Constructor for class org.intermine.web.autocompletion.LuceneSearchEngine

LuceneSearchEngine constructor put the indexes to memory and creates an keyword analyser

M

MailAction - Interface in org.intermine.web.context

The type of objects that can send themselves with an Emailer.

MailDaemon - Class in org.intermine.web.context

An runnable that will send emails delivered over a concurrent queue.

MailDaemon(ArrayBlockingQueue<MailAction>, Emailer) - Constructor for class org.intermine.web.context.MailDaemon

Create a MailDaemon

mailinglist - Variable in class org.intermine.web.struts.CreateAccountForm

MailUtils - Class in org.intermine.util

Mail utilities for the webapp.

main(String[]) - Static method in class org.intermine.sql.query.Query

A testing method - converts the argument into a Query object, and then converts it back to a String again.

main(String[]) - Static method in class org.intermine.web.commandline.PerformanceTester

.

MAIN - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle

The first part of a page title.

MainHelper - Class in org.intermine.api.query

Helper methods for main controller and main action

MainHelper.RangeConfig - Class in org.intermine.api.query

MainHelper.SummaryConfig - Class in org.intermine.api.query

Controls access to configuration information on which fields should be summarised as a count of occurrences.

makeAnatomyTerm(String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

phenotype annotation creates and stores anatomy terms.

makeAnatomyTerm(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

makeBEDRecord(SequenceFeature) - Static method in class org.intermine.bio.web.export.BEDUtil

Create a BEDRecord from a LocatedSequenceFeature.

makeBEDRecord(SequenceFeature, boolean) - Static method in class org.intermine.bio.web.export.BEDUtil

Create a BEDRecord from a LocatedSequenceFeature.

makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Make a new feature

makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

copied from FlyBaseProcessor Make a new feature

makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Make a new feature

makeFeatureData(int, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Create and store a new Item, returning a FeatureData object for the feature.

makeFeatureData(int, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Create and store a new Item, returning a FeatureData object for the feature.

makeForward(ActionMapping, HttpServletRequest, PagedTable) - Method in class org.intermine.web.struts.ChangeTableAction

Create a forward with parameters setting start item and page size.

makeGAFRecord(SequenceFeature) - Static method in class org.intermine.bio.web.export.GAFUtil

Create a GAFRecord from a LocatedSequenceFeature.

makeGFF3Record(SequenceFeature, Map<String, String>, String, Map<String, List<String>>) - Static method in class org.intermine.bio.web.export.GFF3Util

Create a GFF3Record from a SequenceFeature.

makeGFF3Record(SequenceFeature, Map<String, String>, String, Map<String, List<String>>, boolean) - Static method in class org.intermine.bio.web.export.GFF3Util

Create a GFF3Record from a SequenceFeature.

makeInteractionExperiment(String, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Return the item identifier of the Interaction Item for the given pubmed id, creating the Item if necessary.

makeItem() - Method in class org.intermine.xml.full.ItemFactory

Make an empty Item with a unique identifier.

makeItem(String) - Method in class org.intermine.xml.full.ItemFactory

Make an empty Item with the given identifier.

makeItem(String, String, String) - Method in class org.intermine.xml.full.ItemFactory

Construct an item from an identifier, a class name and the names of implemented classes

makeItem(FastPathObject) - Method in class org.intermine.xml.full.ItemFactory

Convert an Object to Item format.

makeItemForClass(String) - Method in class org.intermine.xml.full.ItemFactory

Construct an item from a class name.

makeItemImpl(FastPathObject, Set<String>) - Method in class org.intermine.xml.full.ItemFactory

Convert an Object to Item format, writing the fields provided in includeFields.

makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.result.QueryResultService

makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService

Make the default JSON output given the HttpResponse's PrintWriter.

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListAppendService

makeList(T, String, Profile, Set<String>) - Method in interface org.intermine.webservice.server.lists.ListMaker

Make the list requested by the user.

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListMakerService

Make the list requested by the user.

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListOperationService

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService

makeLocation(String, String, int, int, int, int) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Make a Location Relation between a LocatedSequenceFeature and a Chromosome.

makeLocation(String, String, String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter

Make a Location between a Feature and a Chromosome.

makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

note: featureId is needed only by modMine Make a Location between a SequenceFeature and a Chromosome.

makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Make a Location between a SequenceFeature and a Chromosome.

makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Make a Location between a SequenceFeature and a Chromosome.

makeMultiTypeConstraint(Model, QueryNode, PathConstraintMultitype) - Static method in class org.intermine.api.query.MainHelper

Construct a new multi-type constraint.

makeNodes(String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper

Given a path, render a set of metadata Nodes to the relevant depth

makeNodes(ClassDescriptor, Set<String>, int, Map<?, ?>, List<String>, boolean) - Method in class org.intermine.web.struts.TreeController

Produce a list of tree nodes for a class and its children, marking as 'open' and recursing on any that appear on the openClasses list.

makePath(String) - Method in class org.intermine.pathquery.PathQuery

Produces a Path object from the given path String, using subclass information from the query.

makePathQueryForBag(InterMineBag, WebConfig, Model) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Create a PathQuery to get the contents of an InterMineBag

makePathQueryForCollection(WebConfig, ObjectStore, InterMineObject, String, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Create a PathQuery to get results for a collection of items from an InterMineObject

makePublication(Integer) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Return the item identifier of the publication Item for the given pubmed id.

makeQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, Map<String, BagQueryResult>) - Static method in class org.intermine.api.query.MainHelper

Converts a PathQuery object into an ObjectStore Query object, and optionally populates a Map from String path in the PathQuery to the object in the Query that represents it.

makeQuery(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor

Make the Lower-level Query object to run from the the higher level PathQuery one.

makeQuery(PathQuery) - Method in class org.intermine.api.query.QueryExecutor

Make an InterMine Query object from a PathQuery.

makeQuery(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Creates an IQL query from a PathQuery.

makeQuery(PathQuery, Map<String, BagQueryResult>, Map<String, QuerySelectable>) - Method in class org.intermine.api.query.WebResultsExecutor

Creates an IQL query from a PathQuery.

makeQueryDateConstraint(QueryField, PathConstraintAttribute) - Static method in class org.intermine.api.query.MainHelper

Make a SimpleConstraint for the given Date Constraint.

makeRangeConstraint(Queryable, QueryNode, PathConstraintRange) - Static method in class org.intermine.api.query.MainHelper

makeRangeConstraint(ConstraintOp, Range, ConstraintOptions, QueryField, QueryField, QueryClass) - Method in class org.intermine.api.query.range.AbstractHelper

Construct a constraint for an individual range, to be combined as per the ConstraintOptions.

makeSelectedNodes(String, String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper

Finds the collection of MetadataNode objects that the model browser needs to display.

makeSequenceItem(GFF3Converter, String) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler

For the given GFF3Converter and sequence identifier, make a new sequence object.

makeSql(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor

Get the SQl that will be run on the database.

makeSql(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Creates an SQL query from a PathQuery.

makeSummaryQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, String, ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, ProfileManager, boolean) - Static method in class org.intermine.api.query.MainHelper

Generate a query from a PathQuery, to summarise a particular column of results.

makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner) - Static method in class org.intermine.api.query.MainHelper

Generate a query from a PathQuery, to summarise a particular column of results.

makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, boolean) - Static method in class org.intermine.api.query.MainHelper

Generate a query from a PathQuery, to summarise a particular column of results.

makeSummaryQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor

Creates a query that returns the summary for a column in a PathQuery.

makeSummaryQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor

makeSummaryQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor

Creates a query that returns the summary for a column in a PathQuery, applying a filter at the database level.

makeWithDifferentBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches

Returns a new ResultsBatches object with a different batch size with some of the data already filled in.

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.model.ModelService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.QueryUploadService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.search.QuickSearch

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.SingleTemplateService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.user.DeregistrationService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService

Make the XML output given the HttpResponse's PrintWriter.

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService

makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService

makeXMLOutput(PrintWriter) - Method in class org.intermine.webservice.server.widget.GraphService

manager - Variable in class org.intermine.api.profile.Profile

map(List<Tag>) - Method in class org.intermine.api.profile.TagMapper

Safely transform a list of tags into a list of string, preserving type information.

map(Iterable<T>, Function<T, R>) - Static method in class org.intermine.webservice.server.core.ListFunctions

Transform a collection of things into a list of other things.

MAP_TEMPLATE - Static variable in class org.intermine.api.config.Constants

template to run to get map of values associated with this mine gene.organism --> gene.homologue.organism

mapLocation - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

mappingExists(String, String) - Method in class org.intermine.api.profile.PreferencesManager

MappingUtil - Class in org.intermine.util

Useful utilities to do with mappings.

MappingUtilChecker<T> - Interface in org.intermine.util

Interface providing the capability to check partial mappings for validity for the MappingUtil.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.ListTrackBinding

Convert a ListTrack to XML and write XML to given writer.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.LoginTrackBinding

Convert a LoginTrack to XML and write XML to given writer.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.QueryTrackBinding

Convert a QueryTrack to XML and write XML to given writer.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.SearchTrackBinding

Convert a SearchTrack to XML and write XML to given writer.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding

Convert a TemplateTrack to XML and write XML to given writer.

marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TrackManagerBinding

Convert all tracks to XML and write XML to given writer.

marshal(InterMineBag) - Method in class org.intermine.api.xml.InterMineBagBinding

Convert an InterMine bag to XML

marshal(InterMineBag, XMLStreamWriter) - Static method in class org.intermine.api.xml.InterMineBagBinding

Convert a InterMineIdBag to XML and write XML to given writer.

marshal(Profile, ObjectStore, XMLStreamWriter, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding

Convert a Profile to XML and write XML to given writer.

marshal(Profile, ObjectStore, XMLStreamWriter, boolean, boolean, boolean, boolean, boolean, boolean, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding

Convert a Profile to XML and write XML to given writer.

marshal(ProfileManager, XMLStreamWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding

Convert the contents of a ProfileManager to XML and write the XML to the given writer.

marshal(SavedQuery, XMLStreamWriter, int) - Static method in class org.intermine.api.xml.SavedQueryBinding

Convert a SavedQuery to XML and write XML to given writer.

marshal(SavedQuery, int) - Static method in class org.intermine.api.xml.SavedQueryBinding

Convert a TemplateQuery to XML

marshal(Profile) - Method in class org.intermine.api.xml.SharedBagBinding

Convert the shared bags to XML

marshal(Profile, XMLStreamWriter) - Static method in class org.intermine.api.xml.SharedBagBinding

Convert the bags shared to the profile given in input and write XML to given writer.

marshal(Tag, XMLStreamWriter) - Static method in class org.intermine.api.xml.TagBinding

Convert a Tag to XML and write XML to given writer.

marshal(PathQuery, String, String, int) - Static method in class org.intermine.pathquery.PathQueryBinding

Convert a PathQuery to XML.

marshal(PathQuery, String, String, XMLStreamWriter, int) - Static method in class org.intermine.pathquery.PathQueryBinding

Marshal to an XMLStreamWriter.

marshal(TemplateQuery, XMLStreamWriter, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding

Convert a TemplateQuery to XML and write XML to given writer.

marshal(TemplateQuery, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding

Convert a TemplateQuery to XML

marshal(Collection<FastPathObject>, Writer) - Method in class org.intermine.util.XmlBinding

Marshal a collection of objects to an XML file.

MassTaggingEvent - Class in org.intermine.api.search

A representation of a notification that multiple tags have been added to a profile, and that we do not (indeed cannot) know what they all are.

MassTaggingEvent() - Constructor for class org.intermine.api.search.MassTaggingEvent

matchesAreIssues() - Method in class org.intermine.api.bag.BagQuery

Return the flag passed to the constructor.

MatchingFieldConfigAction - Class in org.intermine.bio.chado.config

A ConfigAction that succeeds only if the value matches a pattern.

MAX - Static variable in class org.intermine.objectstore.query.QueryFunction

Maximum value of a number of rows

max - Variable in class org.intermine.objectstore.query.ResultsInfo

MAX - Static variable in class org.intermine.sql.query.Function

MAX(v) aggregate function - takes one operand.

MAX_BAG_INLINE_SIZE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

The maximum size a bag in a BagConstraint can be before we consider using a temporary table instead.

MAX_CODE - Static variable in class org.intermine.pathquery.PathQuery

The highest code value a constraint may be assigned.

MAX_CONSTRAINTS - Static variable in class org.intermine.pathquery.PathQuery

The maximum number of coded constraints a PathQuery may hold.

MAX_HINT_DISPLAY - Static variable in class org.intermine.web.logic.help.HintManager

The maximum number of times a particular hint should be displayed in a session.

MAX_HITS - Static variable in class org.intermine.api.lucene.KeywordSearch

maximum number of hits returned

MAX_LINESETS - Static variable in class org.intermine.sql.precompute.OptimiserCache

Maximum number of cache linesets in the cache.

MAX_NOT_LOGGED_BAG_SIZE - Static variable in class org.intermine.web.logic.Constants

Maximum size a bag should have if the user is not logged in (to save memory)

MAX_ROWS - Static variable in class org.intermine.task.RunIqlQueryTask

maxLimit - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

maxOffset - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

maxP - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

maxQueryParseTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

maxSize - Variable in class org.intermine.objectstore.query.ResultsBatches

maxSummaryValues - Variable in class org.intermine.api.template.TemplateSummariser

maxTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

maxValues - Variable in class org.intermine.objectstore.ObjectStoreSummary

MemoryOutput - Class in org.intermine.webservice.server.output

Implementation of Output that saves data to memory.

MemoryOutput() - Constructor for class org.intermine.webservice.server.output.MemoryOutput

Constructor

MemoryQueryStore - Class in org.intermine.api.query

An in-memory implementation of a query store.

MemoryQueryStore(int) - Constructor for class org.intermine.api.query.MemoryQueryStore

merge(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Finds all the possible uses of a given precomputed table in the query, and returns them as a Set of new Queries.

merge(ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Merge one or more lists into a new list.

merge(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Merge one or more lists into a new list.

merge(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Merge one or more lists into a new list.

merge(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Merge one or more lists into a new list.

mergeAttributes(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger

Merge the attributes of a target model class descriptor original with the attributes present in class descriptor merge.

mergeClass(ClassDescriptor, ClassDescriptor, Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

Merge the attributes, collections and references from ClassDescriptor merge into the ClassDescriptor original.

mergeCollections(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger

Merge the collections of a target model class descriptor original with the collections present in class descriptor merge.

mergeGroupBy(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Tries to match a PrecomputedTable with a GROUP BY clause to this query.

mergeModel(Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

'Merges' the information from the set of ClassDescriptors classes into the model target.

mergeModelFromFiles(File, List<File>, ModelParser) - Static method in class org.intermine.modelproduction.ModelFileMerger

Merges a model from a core model file and a list of additions files.

mergeMultiple(Set<PrecomputedTable>, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Iteratively calls merge on query with all the PrecomputedTables in a Set, returning the results in a Map from the PrecomputedTable to the Set that merge returns.

mergeProfiles(Profile, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler

Merge two profiles together.

mergeReferences(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger

Merge the references of a target model class descriptor original with the references present in class descriptor merge.

MessageFormat - Enum in org.intermine.web.struts.oauth2

MESSAGES - Static variable in class org.intermine.web.logic.Constants

Session attribute that temporarily holds a Vector of messages that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows message after redirect).

METADATA_TABLE - Static variable in class org.intermine.modelproduction.MetadataManager

Name of the metadata table (created by TorqueModelOutput)

MetadataManager - Class in org.intermine.modelproduction

Class to handle persistence of an intermine objectstore's metadata to the objectstore's database

MetadataManager.LargeObjectInputStream - Class in org.intermine.modelproduction

Class providing an InputStream interface to read a value from the database.

MetadataManager.LargeObjectInputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream

Constructor.

MetadataManager.LargeObjectInputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream

Constructor.

MetadataManager.LargeObjectOutputStream - Class in org.intermine.modelproduction

OutputStream class that writes to a large object in the database.

MetadataManager.LargeObjectOutputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream

Constructs a new object.

MetadataManager.LargeObjectOutputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream

Constructs a new object.

MetadataNode - Class in org.intermine.web.logic.query

Node used in displaying metadata

MetadataNode(String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile) - Constructor for class org.intermine.web.logic.query.MetadataNode

Constructor for a root node

MetadataNode(MetadataNode, String, String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, Boolean) - Constructor for class org.intermine.web.logic.query.MetadataNode

Constructor for a non-root node

methodRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

MgiIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion

ID resolver for MGI genes.

MgiIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory

Construct without SO term of the feature type.

MgiIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory

Construct with SO term of the feature type.

MigrationMapping - Class in org.intermine.web.struts.oauth2

A simple record that contains mapping information about the old id of a user.

MigrationMapping(String, String) - Constructor for class org.intermine.web.struts.oauth2.MigrationMapping

Construct a mapping for Google OpenID migration.

MIN - Static variable in class org.intermine.objectstore.query.QueryFunction

Mininum value of a number of rows

min - Variable in class org.intermine.objectstore.query.ResultsInfo

MIN - Static variable in class org.intermine.sql.query.Function

MIN(v) aggregate function - takes one operand.

MIN_CODE - Static variable in class org.intermine.pathquery.PathQuery

The lowest code value a constraint may be assigned.

MIN_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

The smallest legal result size you can request

minBagTableSize - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Mine - Interface in org.intermine.api.mines

The type of objects that represent InterMine instances.

MineRequester - Interface in org.intermine.api.mines

The type of objects that can request data from mines.

MinimalJsonIterator - Class in org.intermine.webservice.server.output

MinimalJsonIterator(Iterator<List<ResultElement>>) - Constructor for class org.intermine.webservice.server.output.MinimalJsonIterator

Constructor

minRows - Variable in class org.intermine.task.PrecomputeTask

minRows - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

minSize - Variable in class org.intermine.objectstore.query.ResultsBatches

MINUS - Static variable in class org.intermine.sql.query.Function

MINUS function - takes two operands.

MISSING_TABLES - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store the missing tables string.

MissingParameterException - Exception in org.intermine.webservice.server.exceptions

MissingParameterException(String) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException

MissingParameterException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException

MockIdResolverFactory - Class in org.intermine.bio.dataconversion

A mock IdResolver factory needed for testing.

MockIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.MockIdResolverFactory

Construct with class name for mock IdResolver

MockItemWriter - Class in org.intermine.dataconversion

Mimic behaviour of an ItemWriter but actually store Items in a Map rather than an ObjectStoreWriter

MockItemWriter(Map<String, Item>) - Constructor for class org.intermine.dataconversion.MockItemWriter

Constructor

MODE_NORMAL - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext

Normal operation - no logging

MODE_VERBOSE - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext

Normal operation, plus logging to stdout

MODE_VERBOSE_LIST - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext

Logs all generated queries to the stdout, without explaining

MODE_VERBOSE_SUMMARY - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext

Summarises all generated queries to the stdout, without explaining

model - Variable in class org.intermine.api.bag.operations.BagOperation

model - Variable in class org.intermine.api.InterMineAPI

model - Variable in class org.intermine.api.results.WebResults

model - Variable in class org.intermine.bio.task.GFF3ConverterTask

model - Variable in class org.intermine.codegen.JavaModelOutput

model - Variable in class org.intermine.dataconversion.ItemToObjectTranslator

model - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

MODEL - Static variable in class org.intermine.modelproduction.MetadataManager

Name of the key under which to store the serialized version of the model

model - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

model - Variable in class org.intermine.task.AnalyseDbTask

model - Variable in class org.intermine.task.ModelOutputTask

model - Variable in class org.intermine.util.XmlBinding

model - Variable in class org.intermine.web.logic.results.InlineResultsTable

model - Variable in class org.intermine.webservice.server.core.JSONService

ModelBrowserHelper - Class in org.intermine.web.logic.querybuilder

Static class holding methods for managing the model browser in the query builder.

ModelBrowserHelper.NodeBuilder - Class in org.intermine.web.logic.querybuilder

An object that will descend through the model and build a tree of metadata nodes.

ModelBrowserHelper.NodeBuilder(boolean, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary, WebConfig) - Constructor for class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder

Construct a NodeBuilder

modelDescriptors - Static variable in class org.intermine.dataloader.DataLoaderHelper

ModelFileMerger - Class in org.intermine.modelproduction

Methods for merging a model from a list of files.

ModelMerger - Class in org.intermine.modelproduction

Merge model additions into a source model to produce a new larger model.

ModelMergerException - Exception in org.intermine.modelproduction

An Exception that may be thrown by ModelMerger methods.

ModelMergerException() - Constructor for exception org.intermine.modelproduction.ModelMergerException

Constructs a ModelMergerException

ModelMergerException(String) - Constructor for exception org.intermine.modelproduction.ModelMergerException

Constructs a ModelMergerException with the specified detail message.

ModelMergerException(Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException

Constructs a ModelMergerException with the specified nested throwable.

ModelMergerException(String, Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException

Constructs a ModelMergerException with the specified detail message and nested throwable.

ModelMergerTask - Class in org.intermine.task

Task to merge a single additions file into an intermine XML model.

ModelMergerTask() - Constructor for class org.intermine.task.ModelMergerTask

modelName - Variable in class org.intermine.task.StoreMetadataTask

ModelOutputTask - Class in org.intermine.task

Creates and runs a ModelOutput process to generate java or config files.

ModelOutputTask() - Constructor for class org.intermine.task.ModelOutputTask

ModelService - Class in org.intermine.webservice.client.services

This class represents a connection to the RESTful resource on an InterMine server which provides information about the service's data model.

ModelService(String, String) - Constructor for class org.intermine.webservice.client.services.ModelService

Please do not instantiate this class yourself directly - instead use the ServiceFactory - this will ensure maintainability of your code.

ModelService - Class in org.intermine.webservice.server.model

Web service that returns a serialised representation of the data model.

ModelService(InterMineAPI) - Constructor for class org.intermine.webservice.server.model.ModelService

Constructor.

ModelServlet - Class in org.intermine.webservice.server.model

Runs ModelService web service.

ModelServlet() - Constructor for class org.intermine.webservice.server.model.ModelServlet

ModelUpdate - Class in org.intermine.api.profile

Update savedquery, savedtemplatequery and savedbag when the model has been changed

ModelUpdate(ObjectStore, ObjectStoreWriter, Model) - Constructor for class org.intermine.api.profile.ModelUpdate

Construct a ModelUpdate for updating items built in the userprofile with the oldModel given in input

ModelUpdateTask - Class in org.intermine.web.task

Task updating savedquery, savedtemplatequery and savedbag in the userprofile (identified by the userProfileAlias) when the model has been changed

ModelUpdateTask() - Constructor for class org.intermine.web.task.ModelUpdateTask

ModEncodeFeatureProcessor - Class in org.intermine.bio.dataconversion

A processor that loads feature referred to by the modENCODE metadata.

ModEncodeFeatureProcessor(ChadoDBConverter, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Create a new ModEncodeFeatureProcessor.

ModEncodeMetaDataProcessor - Class in org.intermine.bio.dataconversion

Create items from the modENCODE metadata extensions to the chado schema.

ModEncodeMetaDataProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Create a new ChadoProcessor object

ModifyBagAction - Class in org.intermine.web.struts

Implementation of Action to modify bags

ModifyBagAction() - Constructor for class org.intermine.web.struts.ModifyBagAction

ModifyBagDetailsAction - Class in org.intermine.web.struts

ModifyBagDetailsAction() - Constructor for class org.intermine.web.struts.ModifyBagDetailsAction

ModifyBagDetailsForm - Class in org.intermine.web.struts

ModifyBagDetailsForm() - Constructor for class org.intermine.web.struts.ModifyBagDetailsForm

Constructor

ModifyBagForm - Class in org.intermine.web.struts

Form bean to used in combining bags

ModifyBagForm() - Constructor for class org.intermine.web.struts.ModifyBagForm

Constructor

ModifyDetails - Class in org.intermine.web.struts

Action to handle events related to displaying Report templates and displayers

ModifyDetails() - Constructor for class org.intermine.web.struts.ModifyDetails

modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagAddingService

Modify the list by adding the tags.

modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagRemovalService

ModifyQueryAction - Class in org.intermine.web.struts

Action that results from a button press on the user profile page.

ModifyQueryAction() - Constructor for class org.intermine.web.struts.ModifyQueryAction

ModifyQueryChangeAction - Class in org.intermine.web.struts

Implementation of Action that modifies a saved query or bag.

ModifyQueryChangeAction() - Constructor for class org.intermine.web.struts.ModifyQueryChangeAction

ModifyQueryForm - Class in org.intermine.web.struts

Form bean to used in combining queries

ModifyQueryForm() - Constructor for class org.intermine.web.struts.ModifyQueryForm

Constructor

ModifySuperUserAction - Class in org.intermine.web.struts

Implementation of Action to modify superuser role

ModifySuperUserAction() - Constructor for class org.intermine.web.struts.ModifySuperUserAction

ModifySuperUserForm - Class in org.intermine.web.struts

Form bean used in user admin page

ModifySuperUserForm() - Constructor for class org.intermine.web.struts.ModifySuperUserForm

Constructor

ModifyTemplateAction - Class in org.intermine.web.struts

Action that results from a button press on the user profile page.

ModifyTemplateAction() - Constructor for class org.intermine.web.struts.ModifyTemplateAction

ModifyTemplateForm - Class in org.intermine.web.struts

Form bean used on the saved template form.

ModifyTemplateForm() - Constructor for class org.intermine.web.struts.ModifyTemplateForm

Constructor

MODMINE_METADATA_CACHE - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store the modMine MetaData cache

MODULE_NAME - Static variable in class org.intermine.webservice.server.WebServiceConstants

Name of module of web services.

MODULO - Static variable in class org.intermine.objectstore.query.QueryExpression

Return the modulo of two expressions, e.g.

MODULO - Static variable in class org.intermine.sql.query.Function

MODULO arithmetic function - takes two operands.

moveColumnLeft(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Move a column left

moveColumnLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Deprecated.

as we don't move columns any more

moveColumnRight(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Move a column right

moveColumnRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Deprecated.

as we don't move columns any more

moveLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange

Shift a Node left in the view

moveRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange

Shift a Node right in the view

moveToRequest(String, HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods

Move an attribute from the session to the request, removing it from the session.

MULTI_PART_FORM - Static variable in class org.intermine.webservice.client.core.ContentType

Content type for multi-part form requests.

MultiPartRequest - Class in org.intermine.webservice.client.core

A class for constructing multi-part form requests.

MultiPartRequest(String) - Constructor for class org.intermine.webservice.client.core.MultiPartRequest

Construct a new request to the given URL.

MultipleInBagConstraint - Class in org.intermine.objectstore.query

Constraint type requiring any of the given QueryEvaluables to be in a given bag.

MultipleInBagConstraint(Collection<?>, List<? extends QueryEvaluable>) - Constructor for class org.intermine.objectstore.query.MultipleInBagConstraint

Constructor for this class.

multipleInBagConstraintToString(SqlGenerator.State, StringBuffer, MultipleInBagConstraint, Query, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a BagConstraint object into a String suitable for putting on an SQL query.

MULTIPLY - Static variable in class org.intermine.objectstore.query.QueryExpression

Multiplication of two numeric fields

MULTIPLY - Static variable in class org.intermine.sql.query.Function

MULTIPLY function - takes two or more operands.

MultiRow<E> - Class in org.intermine.api.results.flatouterjoins

A subclass of ArrayList returned by the ResultsFlatOuterJoinsImpl indicating a row that can be represented as multiple rows because of collections.

MultiRow() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow

MultiRow(Collection<? extends E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow

MultiRowFirstValue<E> - Class in org.intermine.api.results.flatouterjoins

An object representing an entry in a MultiRow - the first instance of this value in a rowspan.

MultiRowFirstValue(E, int) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

Constructor.

MultiRowLaterValue<E> - Class in org.intermine.api.results.flatouterjoins

An object representing an entry in a MultiRow - entries other than the first value of the rowspan.

MultiRowLaterValue(MultiRowFirstValue<E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowLaterValue

Constructor - should only really be called from MultiRowFirstValue.

MultiRowValue<E> - Class in org.intermine.api.results.flatouterjoins

An object representing an entry in a MultiRow.

MultiRowValue() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowValue

multiValueAttribute - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

MYMINE_PAGE - Static variable in class org.intermine.web.logic.Constants

Session attribute, name of tab selected on MyMine page.

MyMineController - Class in org.intermine.web.struts

Tiles controller for history tile (page).

MyMineController() - Constructor for class org.intermine.web.struts.MyMineController

N

n - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout

Number of milliseconds before timeout.

name - Variable in class org.intermine.api.results.Column

name - Variable in class org.intermine.sql.precompute.PrecomputedTable

name - Variable in class org.intermine.sql.query.Field

name - Variable in class org.intermine.sql.query.Table

name - Variable in class org.intermine.template.TemplateQuery

Template query name.

name - Variable in class org.intermine.util.ReferenceMap

name - Variable in class org.intermine.xml.full.ReferenceList

NAME_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

The name of the new list

NAME_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService

Name of name parameter

namespaceToId - Variable in class org.intermine.dataconversion.ItemToObjectTranslator

nameToTerm - Variable in class org.intermine.bio.dataconversion.OboConverter

NameUtil - Class in org.intermine.api.util

Utility methods for naming queries and lists.

NavigationBarTag - Class in org.intermine.web.tags.table

Class implementing rendering of html of navigation bar.

NavigationBarTag() - Constructor for class org.intermine.web.tags.table.NavigationBarTag

NCBIFastaLoaderTask - Class in org.intermine.bio.dataconversion

A loader that works for FASTA files with an NCBI formatted header: http://www.ncbi.nlm.nih.gov/blast/fasta.shtml http://en.wikipedia.org/wiki/Fasta_format

NCBIFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.NCBIFastaLoaderTask

NcbiGeneInfoParser - Class in org.intermine.bio.dataconversion

Parse NCBI Entrez gene_info file and return data structure for each row for later processing.

NcbiGeneInfoParser(Reader, Set<String>) - Constructor for class org.intermine.bio.dataconversion.NcbiGeneInfoParser

Construct the parser with the file to read, the input file can be for a single taxon or for multiple.

needsDistinct(Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Returns true if this query requires a DISTINCT keyword in the generated SQL.

negate() - Method in class org.intermine.api.query.range.ConstraintOptions

Return a new constraint set with each ConstraintOp negated.

negate() - Method in class org.intermine.objectstore.query.Constraint

Negate this constraint. i.e equals becomes not equals.

negateAndSwap() - Method in class org.intermine.api.query.range.ConstraintOptions

Return a new constraint set with each ConstraintOp negated, and the left and right fields swapped.

neq(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be not equal to a value.

NEVER_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer

NEW_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput

The request parameter for the new name

NEW_TEMPLATE - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the status new template

newBagName - Variable in class org.intermine.web.struts.ModifyBagForm

newBagName - Variable in class org.intermine.web.struts.SaveBagForm

newBagType - Variable in class org.intermine.web.struts.TriageBagForm

newConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Add a new constraint to the query.

NewDeletionTokenService - Class in org.intermine.webservice.server.user

A service that issues a deletion token to a user who intends to delete their profile.

NewDeletionTokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewDeletionTokenService

newId(String) - Method in class org.intermine.dataconversion.DataConverter

Generate an identifier for an item, assign ids sequentially with a different alias per class, e.g.

newpassword - Variable in class org.intermine.web.struts.PasswordResetForm

newpassword2 - Variable in class org.intermine.web.struts.PasswordResetForm

newPathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate

newQuery(String, HttpSession) - Static method in class org.intermine.web.struts.QueryClassSelectAction

Add a new query, based on the specified class, to the session.

newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.ReferenceMap

Private method to create a new ReferenceWithKey object.

newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.SoftReferenceMap

Returns a new SoftReferenceWithKey object for the given objects.

newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.WeakReferenceMap

Returns a new WeakReferenceWithKey object for the given objects.

NewUserService - Class in org.intermine.webservice.server.user

Service for creating a new user.

NewUserService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewUserService

Constructor.

NewUserServlet - Class in org.intermine.webservice.server.user

Servlet for handing off requests to the a NewUserService.

NewUserServlet() - Constructor for class org.intermine.webservice.server.user.NewUserServlet

next() - Method in class org.intermine.api.results.ExportResultsIterator

next() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

next() - Method in class org.intermine.util.CombinedIterator

next() - Method in class org.intermine.util.ObjectPipe

next() - Method in class org.intermine.util.SynchronisedIterator

next() - Method in class org.intermine.webservice.client.results.Page

Get the next page.

next() - Method in class org.intermine.webservice.server.core.TableRowIterator

next() - Method in class org.intermine.webservice.server.output.FilteringResultIterator

next() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator

next() - Method in class org.intermine.webservice.server.output.JSONResultsIterator

next() - Method in class org.intermine.webservice.server.output.JSONRowIterator

next() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator

nextPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Go to the next page

NO_ALIASES_ALL_FIELDS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

I DON'T KNOW

NO_BAGS - Static variable in class org.intermine.api.profile.Profile

Empty typed map holding no bags - useful when creating profiles.

NO_NOTXML - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store the noNotXml string.

NO_QUERIES - Static variable in class org.intermine.api.profile.Profile

Empty typed map holding no saved queries - useful when creating profiles.

NO_SPAM - Static variable in class org.intermine.web.logic.Constants

The preference set if the user does not like lots of emails

NO_TEMPLATES - Static variable in class org.intermine.api.profile.Profile

Empty typed map holding no templates - useful when creating profiles.

NoContent - Exception in org.intermine.api.bag.operations

NoContent() - Constructor for exception org.intermine.api.bag.operations.NoContent

Constructor

NoContentException - Exception in org.intermine.webservice.server.exceptions

The NoContentException is thrown by a service when the resource requested exists but has an empty representation.

NoContentException(String) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException

NoContentException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException

NoContentException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException

Node - Class in org.intermine.pathquery

Superclass of left and right nodes

Node(String) - Constructor for class org.intermine.pathquery.Node

Constructor for a root node

Node(Node, String, boolean) - Constructor for class org.intermine.pathquery.Node

Constructor for a non-root node.

nodeToString(Query, Object, List<Object>, Set<QueryObjectPathExpression>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts an Object into a String.

NONCES - Static variable in class org.intermine.web.logic.Constants

The replay-attack prevention nonces

noneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be NOT ONE OF a collection of values.

NonUniqueName - Exception in org.intermine.api.bag.operations

Exception for non-unique name

NonUniqueName(String) - Constructor for exception org.intermine.api.bag.operations.NonUniqueName

NoServiceException - Exception in org.intermine.webservice.server.core

Exception to throw to signal that there is no service bound to a particular method on a particular endpoint.

NoServiceException() - Constructor for exception org.intermine.webservice.server.core.NoServiceException

NOT_ACCEPTABLE - Static variable in class org.intermine.webservice.server.output.Output

Request will only accept content in a format we cannot provide.

NOT_EQUAL - Static variable in class org.intermine.sql.query.AbstractValue

Describes one AbstractValue as being definitely not equal to another AbstractValue.

NotAcceptableException - Exception in org.intermine.webservice.server.exceptions

NotAcceptableException() - Constructor for exception org.intermine.webservice.server.exceptions.NotAcceptableException

Construct a NotAcceptableException

notAnalysed - Variable in class org.intermine.web.logic.widget.Widget

NotConnectedException - Exception in org.intermine.webservice.client.exceptions

The NotConnectedException is thrown when some method requiring opened connection was called on closed HttpConnection.

NotConnectedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.NotConnectedException

NotConnectedException() - Constructor for exception org.intermine.webservice.client.exceptions.NotConnectedException

Default constructor.

NotConstraint - Class in org.intermine.sql.query

A representation of a constraint that is represented here as the inverse of another Constraint.

NotConstraint(AbstractConstraint) - Constructor for class org.intermine.sql.query.NotConstraint

Constructor for a NotConstraint object.

NotCurrent - Exception in org.intermine.api.bag.operations

NotCurrent() - Constructor for exception org.intermine.api.bag.operations.NotCurrent

Constructor

notEqualTo(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare this value of this AbstractValue with another to see if it is not equal.

notEqualToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be not equal to a loopPath.

NotImplementedException - Exception in org.intermine.webservice.client.exceptions

The NotImplementedException is thrown by a service when an attempt is made to send a request that is not supported by the target service.

NotImplementedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException

NotImplementedException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException

NotImplementedException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException

NotImplementedException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException

NotImplementedException - Exception in org.intermine.webservice.server.exceptions

NotImplementedException(Class<?>, String) - Constructor for exception org.intermine.webservice.server.exceptions.NotImplementedException

notIn(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be NOT IN a named bag.

notInIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be NOT IN a collection of ids.

notLike(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be NOT LIKE a value.

NotPresentException - Exception in org.intermine.api.query

NotPresentException(String) - Constructor for exception org.intermine.api.query.NotPresentException

NotXmlParser - Class in org.intermine.objectstore.intermine

Parses a String suitable for storing in the OBJECT field of database tables into an Object.

NotXmlRenderer - Class in org.intermine.objectstore.intermine

Render on object into a String suitable for storing in the OBJECT field of database tables.

NULL_MODEL_ITEM_FACTORY - Static variable in class org.intermine.xml.full.ItemFactory

An ItemFactory constructed with no Model, so the Items it creates do no type checking.

NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

NULL_VALUE - Static variable in class org.intermine.util.ReferenceMap

nullConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

NullFirstComparator - Class in org.intermine.util

A Comparator that uses the natural ordering of elements implementing Comparable, plus null is allowed and always before all other elements.

NullMailer - Class in org.intermine.web.context

An emailer that doesn't send emails, but does log what it has been asked to do.

NullMailer() - Constructor for class org.intermine.web.context.NullMailer

Get a new NullMailer

NullMailer(Properties) - Constructor for class org.intermine.web.context.NullMailer

Get a null mailer with certain properties.

NUMBER_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint

O

OAUTH2_PROVIDERS - Static variable in class org.intermine.web.logic.Constants

The key under which OAuth2 providers are stored

OAuthProvider - Interface in org.intermine.web.struts.oauth2

A description of an OAuth Provider that we can use as a source of identity information.

obj - Variable in class org.intermine.objectstore.query.ClassConstraint

obj - Variable in class org.intermine.objectstore.query.ContainsConstraint

obj - Variable in class org.intermine.objectstore.query.QueryFunction

ObjectDescription - Class in org.intermine.dataloader

Object class used by DataTracker for data tracking.

ObjectDescription() - Constructor for class org.intermine.dataloader.ObjectDescription

Constructs a new ObjectDescription.

ObjectDescription(ObjectDescription) - Constructor for class org.intermine.dataloader.ObjectDescription

Constructs a new ObjectDescription from an existing one.

ObjectDetails - Class in org.intermine.api.beans

An object that describes an object.

ObjectDetails() - Constructor for class org.intermine.api.beans.ObjectDetails

ObjectDetailsBeanInfo - Class in org.intermine.api.beans

An object that describes the ObjectDetails bean and supports DWR serialization.

ObjectDetailsBeanInfo() - Constructor for class org.intermine.api.beans.ObjectDetailsBeanInfo

ObjectPipe<E> - Class in org.intermine.util

This is a rather simple implementation of a queue designed for passing objects from one Thread to another to form a pipeline.

ObjectPipe() - Constructor for class org.intermine.util.ObjectPipe

Construct an ObjectPipe with a default maximum buffer size.

ObjectPipe(int) - Constructor for class org.intermine.util.ObjectPipe

Construct an ObjectPipe with a certain maximum buffer size.

objectPrimaryKeyNotNull(Model, InterMineObject, ClassDescriptor, PrimaryKey, Source, IntToIntMap) - Static method in class org.intermine.dataloader.DataLoaderHelper

Look a the values of the given primary key in the object and return true if and only if some part of the primary key is null.

ObjectRequest - Class in org.intermine.api.mines

A generic container for a request for information about an object.

ObjectRequest(String, String) - Constructor for class org.intermine.api.mines.ObjectRequest

Define a new object request.

Objects - Class in org.intermine.api.data

Helper class to encapsulate some common logic regarding the use of data objects.

objectStore - Variable in class org.intermine.api.InterMineAPI

ObjectStore - Interface in org.intermine.objectstore

Gets the Results of a Query from an underlying store.

ObjectStoreAbstractImpl - Class in org.intermine.objectstore

Abstract implementation of the ObjectStore interface.

ObjectStoreAbstractImpl() - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl

No-arg constructor for testing purposes

ObjectStoreAbstractImpl(Model) - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl

Construct an ObjectStore with some metadata

ObjectStoreBag - Class in org.intermine.objectstore.query

Object representing a collection of objects which have been stored in the database.

ObjectStoreBag(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBag

Constructs a new ObjectStoreBag.

ObjectStoreBagCombination - Class in org.intermine.objectstore.query

Object representing a combination of ObjectStoreBags.

ObjectStoreBagCombination(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagCombination

Constructs a new ObjectStoreBagCombination.

ObjectStoreBagsForObject - Class in org.intermine.objectstore.query

Object representing a query to fetch ObjectStoreBag IDs for ObjectStoreBags that contain a certain value.

ObjectStoreBagsForObject(Integer) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject

Constructs a new ObjectStoreBagsForObject with no limit on the ObjectStoreBags returned.

ObjectStoreBagsForObject(Integer, Collection<ObjectStoreBag>) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject

Constructs a new ObjectStoreBagsForObject with a limited set of ObjectStoreBags that can be present in the results.

ObjectStoreDataLoader - Class in org.intermine.dataloader

Loads information from an ObjectStore into the InterMine database.

ObjectStoreDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.ObjectStoreDataLoader

Construct an ObjectStoreDataLoader

ObjectStoreDataLoaderTask - Class in org.intermine.dataloader

Uses an IntegrationWriter to load data from another ObjectStore.

ObjectStoreDataLoaderTask() - Constructor for class org.intermine.dataloader.ObjectStoreDataLoaderTask

ObjectStoreException - Exception in org.intermine.objectstore

An Exception that may be thrown by an ObjectStore indicating a fatal error.

ObjectStoreException() - Constructor for exception org.intermine.objectstore.ObjectStoreException

Constructs an ObjectStoreException

ObjectStoreException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreException

Constructs an ObjectStoreException with the specified detail message.

ObjectStoreException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException

Constructs an ObjectStoreException with the specified nested throwable.

ObjectStoreException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException

Constructs an ObjectStoreException with the specified detail message and nested throwable.

ObjectStoreFactory - Class in org.intermine.objectstore

Produce ObjectStores

ObjectStoreFastCollectionsForTranslatorImpl - Class in org.intermine.objectstore.fastcollections

Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides, written for the translating objectstore.

ObjectStoreFastCollectionsForTranslatorImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Creates an instance, from another ObjectStore instance.

ObjectStoreFastCollectionsImpl - Class in org.intermine.objectstore.fastcollections

Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides.

ObjectStoreFastCollectionsImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Creates an instance, from another ObjectStore instance.

ObjectStoreInterMineImpl - Class in org.intermine.objectstore.intermine

An SQL-backed implementation of the ObjectStore interface.

ObjectStoreInterMineImpl(Model) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Constructs an ObjectStoreInterMineImpl - for use by the ObjectStoreWriter only!

ObjectStoreInterMineImpl(Database, DatabaseSchema) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Constructs an ObjectStoreInterMineImpl, with a schema.

ObjectStoreInterMineImpl.BagTableToRemove - Class in org.intermine.objectstore.intermine

Class describing a temporary bag table, which can be removed.

ObjectStoreItemWriter - Class in org.intermine.dataconversion

Stores Items in an objectstore.

ObjectStoreItemWriter(ObjectStoreWriter) - Constructor for class org.intermine.dataconversion.ObjectStoreItemWriter

Constructs the ItemWriter with an ObjectStoreWriter.

ObjectStoreLimitReachedException - Exception in org.intermine.objectstore

An exception that may be thrown by the objectstore, when an access is made outside the allowable maximum query size.

ObjectStoreLimitReachedException() - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException

Constructs an ObjectStoreLimitReachedException.

ObjectStoreLimitReachedException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException

Constructs an ObjectStoreLimitReachedException with the specified detail message.

ObjectStorePassthruImpl - Class in org.intermine.objectstore

A generic ObjectStore that passes through every request to an underlying ObjectStore.

ObjectStorePassthruImpl(ObjectStore) - Constructor for class org.intermine.objectstore.ObjectStorePassthruImpl

Creates an instance, from another ObjectStore instance.

ObjectStoreQueryDurationException - Exception in org.intermine.objectstore

An Exception thrown if the estimated time to complete a query is greater than the maximum permitted.

ObjectStoreQueryDurationException() - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException

Create a new ObjectStoreQueryDurationException.

ObjectStoreQueryDurationException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException

Create a new ObjectStoreQueryDurationException with the given detail message.

ObjectStoreQueryDurationException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException

Create a new ObjectStoreQueryDurationException with the specified nested throwable.

ObjectStoreQueryDurationException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException

Create a new ObjectStoreQueryDurationException with the specified detail message and nested throwable.

ObjectStoreSafeImpl - Class in org.intermine.objectstore.safe

Provides a safe implementation of an objectstore - that is, an implementation that works correctly if passed a Query object that has been modified since being used previously.

ObjectStoreSafeImpl(ObjectStore) - Constructor for class org.intermine.objectstore.safe.ObjectStoreSafeImpl

Creates an instance, from another ObjectStore instance.

ObjectStoreSummary - Class in org.intermine.objectstore

A summary of the data in an ObjectStore

ObjectStoreSummary(ObjectStore, Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary

Construct a summary from by running queries in the ObjectStore.

ObjectStoreSummary(Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary

Construct a summary from a properties object.

ObjectStoreTranslatingImpl - Class in org.intermine.objectstore.translating

ObjectStore that transparently translates incoming queries and outgoing objects

ObjectStoreTranslatingImpl(Model, ObjectStore, Translator) - Constructor for class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl

Constructor

objectStoreWriter - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

objectStoreWriter - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

ObjectStoreWriter - Interface in org.intermine.objectstore

Store, update, and delete objects

ObjectStoreWriterFactory - Class in org.intermine.objectstore

Produce ObjectStoreWriters

ObjectStoreWriterInterMineImpl - Class in org.intermine.objectstore.intermine

An SQL-backed implementation of the ObjectStoreWriter interface, backed by ObjectStoreInterMineImpl.

ObjectStoreWriterInterMineImpl(ObjectStore) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Constructor for this ObjectStoreWriter.

objectToString(StringBuffer, Object) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts an Object to a String, in a form suitable for SQL.

objectToString(Object) - Static method in class org.intermine.sql.DatabaseUtil

Generate an SQL compatible representation of an object.

ObjectTrailController - Class in org.intermine.web.struts

Controller for the object trail tile.

ObjectTrailController() - Constructor for class org.intermine.web.struts.ObjectTrailController

ObjectTrailController.TrailElement - Class in org.intermine.web.struts

Bean passed to JSP to represent an element in the trail.

ObjectViewController - Class in org.intermine.web.struts

Controls display of data in results tables.

ObjectViewController() - Constructor for class org.intermine.web.struts.ObjectViewController

OboConverter - Class in org.intermine.bio.dataconversion

Convert tree of OboTerms into Items.

OboConverter(ItemWriter, Model, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.OboConverter

Constructor for this class.

OboConverterTask - Class in org.intermine.bio.task

Initiates retrieval and conversion of data from a source database

OboConverterTask() - Constructor for class org.intermine.bio.task.OboConverterTask

OboParser - Class in org.intermine.bio.ontology

OboParser() - Constructor for class org.intermine.bio.ontology.OboParser

OboRelation - Class in org.intermine.bio.ontology

Object representing an OBO relation.

OboRelation(String, String, OboTypeDefinition) - Constructor for class org.intermine.bio.ontology.OboRelation

Constructor

oboRelations - Variable in class org.intermine.bio.dataconversion.OboConverter

OboTerm - Class in org.intermine.bio.ontology

Extension of DagTerm that adds a namespace attribute that is specific to the OBO format.

OboTerm(String, String) - Constructor for class org.intermine.bio.ontology.OboTerm

Construct with an id and name.

OboTerm(String) - Constructor for class org.intermine.bio.ontology.OboTerm

Construct with an id, only used for uberon xrefs

oboTerms - Variable in class org.intermine.bio.dataconversion.OboConverter

OboTermSynonym - Class in org.intermine.bio.ontology

Object representing aa OboTerm synonym.

OboTermSynonym(String, String) - Constructor for class org.intermine.bio.ontology.OboTermSynonym

Create a new instance of DagTermSynonym.

OboTypeDefinition - Class in org.intermine.bio.ontology

Class representing an OBO type.

OboTypeDefinition(String, String, boolean) - Constructor for class org.intermine.bio.ontology.OboTypeDefinition

The constructor

officialName - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

officialSymbol - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

offset - Variable in class org.intermine.objectstore.query.ClobAccess

offset - Variable in class org.intermine.sql.query.Query

OLD - Static variable in class org.intermine.api.profile.ModelUpdate

suffix used to rename the previous items

OLD_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput

The request parameter for the old name

oldModel - Variable in class org.intermine.api.profile.PathQueryUpdate

ONE - Static variable in class org.intermine.web.logic.widget.ErrorCorrection

oneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be ONE OF a collection of values.

ontology - Variable in class org.intermine.bio.dataconversion.OboConverter

OntologyIdResolverFactory - Class in org.intermine.bio.dataconversion

OntologyIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.OntologyIdResolverFactory

Construct with SO term of the feature type to read from chado database.

op - Variable in class org.intermine.objectstore.query.Constraint

op - Variable in class org.intermine.objectstore.query.QueryFunction

op - Variable in class org.intermine.pathquery.PathConstraint

OPENID_PROVIDERS - Static variable in class org.intermine.web.logic.Constants

The key for the open-id providers located in the servlet context.

OpenIDAuthenticator - Class in org.intermine.web.logic.login

Authenticate requests using OpenID

OpenIDAuthenticator() - Constructor for class org.intermine.web.logic.login.OpenIDAuthenticator

Default constructor.

openResource(String) - Method in class org.intermine.web.logic.ClassResourceOpener

openResource(String) - Method in interface org.intermine.web.logic.ResourceOpener

Open a resource by name, and return an InputStream to it.

openResource(String) - Method in class org.intermine.web.struts.ResourceFinder

operands - Variable in class org.intermine.sql.query.Function

operate() - Method in class org.intermine.api.bag.operations.BagOperation

Perform this bag operation.

operate() - Method in interface org.intermine.api.bag.operations.BagProducer

operation - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

operation - Variable in class org.intermine.sql.query.Constraint

operation - Variable in class org.intermine.sql.query.Function

operationButton - Variable in class org.intermine.web.struts.SaveBagForm

operator - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

OPPOSITE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as being opposite to each other.

optimise - Variable in class org.intermine.objectstore.query.Results

optimise(String, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query represented in the String, given the database.

optimise(String, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query represented in the String, given the database.

optimise(Query, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query, given the database.

optimise(Query, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query, given the database.

optimise(String, Query, Object, Connection, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query represented in the String and Query, given the Connection and an object to lookup a PrecomputedTable

OptimiserCache - Class in org.intermine.sql.precompute

A class that provides an implementation of a cache for String-based SQL query optimisation.

OptimiserCache() - Constructor for class org.intermine.sql.precompute.OptimiserCache

Constructor for this object.

OptimiserCacheLine - Class in org.intermine.sql.precompute

A class that provides an implementation of a cache line, encapsulating several pieces of data.

OptimiserCacheLine(String, int, String) - Constructor for class org.intermine.sql.precompute.OptimiserCacheLine

Constructor for this object.

OptimiserMappingChecker - Class in org.intermine.sql.precompute

Class for checking partial mappings for validity for the MappingUtil.

OptimiserMappingChecker(Set<AbstractConstraint>, Set<AbstractConstraint>) - Constructor for class org.intermine.sql.precompute.OptimiserMappingChecker

Constructor.

optimiseWith(String, Query, Database, Connection, QueryOptimiserContext, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Runs the optimiser through the query repesented in the String and Query, given the Connection and a set of PrecomputedTables.

OR - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints as following "constraint 1 OR constraint 2 IS TRUE".

orderBags(Map<String, InterMineBag>) - Method in class org.intermine.api.bag.BagManager

Order a map of bags by im:order:n tag

orderBy - Variable in class org.intermine.sql.query.Query

ORDERBY_FIELD - Static variable in class org.intermine.sql.precompute.PrecomputedTable

The name of the field that is generated as the order by field

orderByField - Variable in class org.intermine.sql.precompute.PrecomputedTable

OrderDescending - Class in org.intermine.objectstore.query

An element that can appear in the ORDER BY clause of a query, to reverse the order.

OrderDescending(QueryOrderable) - Constructor for class org.intermine.objectstore.query.OrderDescending

Creates a new OrderDescending object from the given QueryOrderable.

OrderDescending - Class in org.intermine.sql.query

A representation of an item that can be present in the ORDER BY section of an SQL query, but ordered descending..

OrderDescending(AbstractValue) - Constructor for class org.intermine.sql.query.OrderDescending

Constructor for OrderDescending.

OrderDirection - Enum in org.intermine.pathquery

An enumeration for the direction of sorting for results.

OrderElement - Class in org.intermine.pathquery

An element of the order by list of a PathQuery, containing a path and a direction.

OrderElement(String, OrderDirection) - Constructor for class org.intermine.pathquery.OrderElement

Constructor, taking a path and a direction.

org.intermine.api - package org.intermine.api

org.intermine.api.bag - package org.intermine.api.bag

org.intermine.api.bag.operations - package org.intermine.api.bag.operations

org.intermine.api.beans - package org.intermine.api.beans

org.intermine.api.config - package org.intermine.api.config

org.intermine.api.data - package org.intermine.api.data

org.intermine.api.idresolution - package org.intermine.api.idresolution

org.intermine.api.lucene - package org.intermine.api.lucene

org.intermine.api.mines - package org.intermine.api.mines

org.intermine.api.profile - package org.intermine.api.profile

org.intermine.api.query - package org.intermine.api.query

org.intermine.api.query.codegen - package org.intermine.api.query.codegen

org.intermine.api.query.range - package org.intermine.api.query.range

org.intermine.api.results - package org.intermine.api.results

org.intermine.api.results.flatouterjoins - package org.intermine.api.results.flatouterjoins

org.intermine.api.search - package org.intermine.api.search

org.intermine.api.tag - package org.intermine.api.tag

org.intermine.api.template - package org.intermine.api.template

org.intermine.api.tracker - package org.intermine.api.tracker

org.intermine.api.tracker.factory - package org.intermine.api.tracker.factory

org.intermine.api.tracker.track - package org.intermine.api.tracker.track

org.intermine.api.tracker.util - package org.intermine.api.tracker.util

org.intermine.api.tracker.xml - package org.intermine.api.tracker.xml

org.intermine.api.types - package org.intermine.api.types

org.intermine.api.util - package org.intermine.api.util

org.intermine.api.xml - package org.intermine.api.xml

org.intermine.bio.chado - package org.intermine.bio.chado

org.intermine.bio.chado.config - package org.intermine.bio.chado.config

org.intermine.bio.dataconversion - package org.intermine.bio.dataconversion

org.intermine.bio.io.bed - package org.intermine.bio.io.bed

org.intermine.bio.io.gaf - package org.intermine.bio.io.gaf

org.intermine.bio.io.gff3 - package org.intermine.bio.io.gff3

org.intermine.bio.ontology - package org.intermine.bio.ontology

org.intermine.bio.postprocess - package org.intermine.bio.postprocess

org.intermine.bio.query.range - package org.intermine.bio.query.range

org.intermine.bio.task - package org.intermine.bio.task

org.intermine.bio.util - package org.intermine.bio.util

org.intermine.bio.web.export - package org.intermine.bio.web.export

org.intermine.codegen - package org.intermine.codegen

org.intermine.dataconversion - package org.intermine.dataconversion

org.intermine.dataloader - package org.intermine.dataloader

org.intermine.dwr - package org.intermine.dwr

org.intermine.model - package org.intermine.model

org.intermine.modelproduction - package org.intermine.modelproduction

org.intermine.objectstore - package org.intermine.objectstore

org.intermine.objectstore.fastcollections - package org.intermine.objectstore.fastcollections

org.intermine.objectstore.intermine - package org.intermine.objectstore.intermine

org.intermine.objectstore.proxy - package org.intermine.objectstore.proxy

org.intermine.objectstore.query - package org.intermine.objectstore.query

org.intermine.objectstore.query.iql - package org.intermine.objectstore.query.iql

org.intermine.objectstore.querygen - package org.intermine.objectstore.querygen

org.intermine.objectstore.safe - package org.intermine.objectstore.safe

org.intermine.objectstore.translating - package org.intermine.objectstore.translating

org.intermine.pathquery - package org.intermine.pathquery

org.intermine.postprocess - package org.intermine.postprocess

org.intermine.sql - package org.intermine.sql

org.intermine.sql.logging - package org.intermine.sql.logging

org.intermine.sql.precompute - package org.intermine.sql.precompute

org.intermine.sql.query - package org.intermine.sql.query

org.intermine.sql.writebatch - package org.intermine.sql.writebatch

org.intermine.task - package org.intermine.task

org.intermine.template - package org.intermine.template

org.intermine.template.xml - package org.intermine.template.xml

org.intermine.util - package org.intermine.util

org.intermine.web.autocompletion - package org.intermine.web.autocompletion

org.intermine.web.bag - package org.intermine.web.bag

org.intermine.web.commandline - package org.intermine.web.commandline

org.intermine.web.context - package org.intermine.web.context

org.intermine.web.displayer - package org.intermine.web.displayer

org.intermine.web.filters - package org.intermine.web.filters

org.intermine.web.logic - package org.intermine.web.logic

org.intermine.web.logic.aspects - package org.intermine.web.logic.aspects

org.intermine.web.logic.bag - package org.intermine.web.logic.bag

org.intermine.web.logic.config - package org.intermine.web.logic.config

org.intermine.web.logic.export - package org.intermine.web.logic.export

org.intermine.web.logic.export.http - package org.intermine.web.logic.export.http

org.intermine.web.logic.export.rowformatters - package org.intermine.web.logic.export.rowformatters

org.intermine.web.logic.export.string - package org.intermine.web.logic.export.string

org.intermine.web.logic.help - package org.intermine.web.logic.help

org.intermine.web.logic.login - package org.intermine.web.logic.login

org.intermine.web.logic.pathqueryresult - package org.intermine.web.logic.pathqueryresult

org.intermine.web.logic.profile - package org.intermine.web.logic.profile

org.intermine.web.logic.query - package org.intermine.web.logic.query

org.intermine.web.logic.querybuilder - package org.intermine.web.logic.querybuilder

org.intermine.web.logic.results - package org.intermine.web.logic.results

org.intermine.web.logic.session - package org.intermine.web.logic.session

org.intermine.web.logic.template - package org.intermine.web.logic.template

org.intermine.web.logic.widget - package org.intermine.web.logic.widget

org.intermine.web.logic.widget.config - package org.intermine.web.logic.widget.config

org.intermine.web.search - package org.intermine.web.search

org.intermine.web.security - package org.intermine.web.security

org.intermine.web.struts - package org.intermine.web.struts

org.intermine.web.struts.oauth2 - package org.intermine.web.struts.oauth2

org.intermine.web.tags.disclosure - package org.intermine.web.tags.disclosure

org.intermine.web.tags.table - package org.intermine.web.tags.table

org.intermine.web.tags.util - package org.intermine.web.tags.util

org.intermine.web.task - package org.intermine.web.task

org.intermine.web.util - package org.intermine.web.util

org.intermine.webservice.client.core - package org.intermine.webservice.client.core

org.intermine.webservice.client.exceptions - package org.intermine.webservice.client.exceptions

org.intermine.webservice.client.lists - package org.intermine.webservice.client.lists

org.intermine.webservice.client.results - package org.intermine.webservice.client.results

org.intermine.webservice.client.services - package org.intermine.webservice.client.services

Contains all InterMine web services at one place.

org.intermine.webservice.client.template - package org.intermine.webservice.client.template

org.intermine.webservice.client.util - package org.intermine.webservice.client.util

org.intermine.webservice.client.widget - package org.intermine.webservice.client.widget

org.intermine.webservice.server - package org.intermine.webservice.server

Intermine and mines derived from Intermine implement RESTfull web services.

org.intermine.webservice.server.branding - package org.intermine.webservice.server.branding

org.intermine.webservice.server.clob - package org.intermine.webservice.server.clob

org.intermine.webservice.server.core - package org.intermine.webservice.server.core

org.intermine.webservice.server.data - package org.intermine.webservice.server.data

org.intermine.webservice.server.exceptions - package org.intermine.webservice.server.exceptions

org.intermine.webservice.server.filter - package org.intermine.webservice.server.filter

org.intermine.webservice.server.idresolution - package org.intermine.webservice.server.idresolution

org.intermine.webservice.server.lists - package org.intermine.webservice.server.lists

org.intermine.webservice.server.model - package org.intermine.webservice.server.model

org.intermine.webservice.server.output - package org.intermine.webservice.server.output

org.intermine.webservice.server.path - package org.intermine.webservice.server.path

org.intermine.webservice.server.query - package org.intermine.webservice.server.query

org.intermine.webservice.server.query.result - package org.intermine.webservice.server.query.result

org.intermine.webservice.server.search - package org.intermine.webservice.server.search

org.intermine.webservice.server.template - package org.intermine.webservice.server.template

org.intermine.webservice.server.template.result - package org.intermine.webservice.server.template.result

org.intermine.webservice.server.user - package org.intermine.webservice.server.user

org.intermine.webservice.server.widget - package org.intermine.webservice.server.widget

org.intermine.xml - package org.intermine.xml

org.intermine.xml.full - package org.intermine.xml.full

OrganismData - Class in org.intermine.bio.util

A class to hold data about one organism.

OrganismRepository - Class in org.intermine.bio.util

A class to hold information about organisms.

organisms - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask

organisms - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

orgIdMainMaps - Variable in class org.intermine.bio.dataconversion.IdResolver

orgIdMaps - Variable in class org.intermine.bio.dataconversion.IdResolver

orgIdSynMaps - Variable in class org.intermine.bio.dataconversion.IdResolver

orgMainMaps - Variable in class org.intermine.bio.dataconversion.IdResolver

orgSynMaps - Variable in class org.intermine.bio.dataconversion.IdResolver

orgTaxonId - Variable in class org.intermine.bio.task.GFF3ConverterTask

origin - Variable in class org.intermine.api.search.OriginatingEvent

originalSql - Variable in class org.intermine.sql.precompute.PrecomputedTable

OriginatingEvent - Class in org.intermine.api.search

A representation of a notification that something has happened that originated at a particular web searchable object.

OriginatingEvent(WebSearchable) - Constructor for class org.intermine.api.search.OriginatingEvent

Constructor.

originatingQuery - Variable in class org.intermine.api.results.ExportResultsIterator

os - Variable in class org.intermine.api.profile.ProfileManager

os - Variable in class org.intermine.api.query.QueryExecutor

os - Variable in class org.intermine.api.template.TemplateSummariser

os - Variable in class org.intermine.bio.postprocess.CalculateLocations

os - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

os - Variable in class org.intermine.bio.postprocess.GoPostprocess

os - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

os - Variable in class org.intermine.objectstore.ObjectStorePassthruImpl

os - Variable in class org.intermine.objectstore.query.ClobAccess

os - Variable in class org.intermine.objectstore.query.ResultsBatches

os - Variable in class org.intermine.objectstore.translating.Translator

os - Variable in class org.intermine.web.logic.widget.Widget

os - Variable in class org.intermine.web.logic.widget.WidgetLdr

os - Variable in class org.intermine.web.task.CreateSearchIndexTask

os - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

OS_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store objectstore format version number.

OS_SUMMARY - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key to use to store the objectstoresummary.properties file.

osAlias - Variable in class org.intermine.web.task.CreateSearchIndexTask

osb - Variable in class org.intermine.objectstore.query.BagConstraint

osName - Variable in class org.intermine.task.PostProcessorTask

osname - Variable in class org.intermine.task.RetrieveMetadataTask

osName - Variable in class org.intermine.task.StoreMetadataTask

oss - Variable in class org.intermine.api.InterMineAPI

osw - Variable in class org.intermine.api.template.TemplateSummariser

osw - Variable in class org.intermine.api.tracker.TrackerDelegate

osw - Variable in class org.intermine.api.tracker.xml.TrackHandler

osw - Variable in class org.intermine.bio.postprocess.CalculateLocations

osw - Variable in class org.intermine.bio.postprocess.CreateLocationOverlapIndex

osw - Variable in class org.intermine.bio.postprocess.CreateReferences

osw - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

osw - Variable in class org.intermine.bio.postprocess.OverlapViewTask

osw - Variable in class org.intermine.bio.postprocess.PopulateChildFeatures

osw - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

osw - Variable in class org.intermine.bio.postprocess.TransferSequences

osw - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

osw - Variable in class org.intermine.postprocess.PostProcessor

osWriter - Variable in class org.intermine.api.profile.TagManager

OTHER - Static variable in class org.intermine.api.bag.BagQueryResult

Key of the Map returned by getIssues() when the input string

OuterJoinStatus - Enum in org.intermine.pathquery

Enumeration for outer join status.

Output - Class in org.intermine.webservice.server.output

Abstract class representing an output of a web service.

Output() - Constructor for class org.intermine.webservice.server.output.Output

output - Variable in class org.intermine.webservice.server.WebService

The response to the outside world.

OUTPUT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Name of format parameter that specifies format of returned results.

outputFile - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask

outputFile - Variable in class org.intermine.task.SummariseObjectStoreTask

outputModelFile - Variable in class org.intermine.task.ModelMergerTask

overlap(CalculateLocations.SimpleLoc, CalculateLocations.SimpleLoc) - Static method in class org.intermine.bio.postprocess.CalculateLocations

Return true if locations of two objects on some parent object have any overlap.

OverlapConstraint - Class in org.intermine.objectstore.query

Represents a constraint comparing two range values on an object.

OverlapConstraint(OverlapRange, ConstraintOp, OverlapRange) - Constructor for class org.intermine.objectstore.query.OverlapConstraint

Construct a constraint.

overlapConstraintToString(SqlGenerator.State, StringBuffer, OverlapConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts an OverlapConstraint to a String suitable for putting in an SQL query.

OverlapRange - Class in org.intermine.objectstore.query

Represents a range value on an object.

OverlapRange(QueryEvaluable, QueryEvaluable, QueryObjectReference) - Constructor for class org.intermine.objectstore.query.OverlapRange

Constructor for this object.

OverlapUtil - Class in org.intermine.bio.postprocess

Utility methods for finding overlaps.

OverlapViewTask - Class in org.intermine.bio.postprocess

A task the replace the sequencefeatureoverlappingfeatures table with a view that uses the bioseg type to calculate the overlaps.

OverlapViewTask(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.OverlapViewTask

Construct a new OverlapViewTask that will change the given object store.

P

Page - Class in org.intermine.webservice.client.results

Object representing a page parameter.

Page(int, int) - Constructor for class org.intermine.webservice.client.results.Page

Construct a new page, specifying a start point and a size.

Page(int) - Constructor for class org.intermine.webservice.client.results.Page

Construct a new page, specifying a start point.

Page - Class in org.intermine.webservice.server.core

Parameter class for passing start and limit arguments to iterators.

Page(int, Integer) - Constructor for class org.intermine.webservice.server.core.Page

Construct a new page.

Page(int) - Constructor for class org.intermine.webservice.server.core.Page

Construct a new page, going from a certain row to the end of the result set.

PagedTable - Class in org.intermine.web.logic.results

Deprecated.

Use web-services instead.

PagedTable(WebTable) - Constructor for class org.intermine.web.logic.results.PagedTable

Deprecated.

Construct a PagedTable with a list of column names

PagedTable(WebTable, int) - Constructor for class org.intermine.web.logic.results.PagedTable

Deprecated.

Construct a PagedTable with a list of column names

pageName - Variable in class org.intermine.web.struts.ModifyBagForm

pageName - Variable in class org.intermine.web.struts.ModifyTemplateForm

PageOutOfRangeException - Exception in org.intermine.web.logic.results

PageOutOfRangeException class

PageOutOfRangeException(String, Throwable) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException

Create a new PageOutOfRangeException.

PageOutOfRangeException(String) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException

Create a new PageOutOfRangeException.

pageSize - Variable in class org.intermine.web.struts.ChangeTableSizeForm

PageTableQueryMonitor - Class in org.intermine.web.logic.query

An implementation of QueryMonitor that maintains a timeout and remembers which PagedTable it is monitoring

PageTableQueryMonitor(int, PagedTable) - Constructor for class org.intermine.web.logic.query.PageTableQueryMonitor

Construct a new instance of QueryMonitorTimeout.

Pair<A,B> - Class in org.intermine.webservice.server.core

A tuple of order two.

Pair(A, B) - Constructor for class org.intermine.webservice.server.core.Pair

Construct a pair of two things

parallel - Variable in class org.intermine.sql.Database

The number of worker threads to use for background SQL statements

ParallelBatchingFetcher - Class in org.intermine.dataloader

Class providing EquivalentObjectFetcher functionality that fetches batches of equivalent objects in parallel to improve performance.

ParallelBatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.ParallelBatchingFetcher

Constructor

ParallelPrecomputer - Class in org.intermine.objectstore.intermine

An object that can perform a set of precomputes in parallel.

ParallelPrecomputer(ObjectStoreInterMineImpl, int) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer

Constructor.

ParallelPrecomputer.Job - Class in org.intermine.objectstore.intermine

Class representing a precomputing job to be performed.

ParallelPrecomputer.Job(String, Query, Collection<? extends QueryNode>, boolean, String) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer.Job

Constructor - takes the same arguments as ObjectStoreInterMineImpl.precompute().

parameterIsRequired(String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser

Declare that a particular parameter is required.

params - Variable in class org.intermine.web.struts.ForwardParameters

Map from parameter name to parameter value.

parent - Variable in class org.intermine.objectstore.query.OverlapRange

parents - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

parse(BufferedReader) - Method in class org.intermine.bio.dataconversion.GFF3Converter

Parse a bufferedReader and process GFF3 record

parse(BufferedReader) - Static method in class org.intermine.bio.io.gff3.GFF3Parser

Read GFF3 lines from a BufferedReader and return an Iterator over the GFF3Records.

parse(String, ObjectStoreInterMineImpl) - Static method in class org.intermine.objectstore.intermine.NotXmlParser

Parse the given NotXml String into an Object.

parse(IqlQuery) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser

Construct a new query by parsing a String.

parse(String, Class<?>) - Static method in class org.intermine.pathquery.ConstraintValueParser

Parses a value.

parse(InputSource, DefaultHandler) - Static method in class org.intermine.util.SAXParser

Parse the an xml file

parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.util.SAXParser

Parse the an xml file

parse(ServletContext, Model) - Static method in class org.intermine.web.logic.config.WebConfig

Parse a WebConfig XML file

parse(ResultsRow<?>) - Method in interface org.intermine.webservice.server.core.ResultRowParser

Parse result row to list of strings.

parse(InputStream) - Static method in class org.intermine.xml.full.FullParser

Parse a InterMine Full XML file

parseConstraints(HttpServletRequest) - Static method in class org.intermine.web.logic.template.Templates

Given a HTTP request, parse out the template values.

parseCsvDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser

Return an Iterator over a comma/tab delimited file.

parseDelimitedReader(Reader, char) - Static method in class org.intermine.util.FormattedTextParser

Return an Iterator over a delimited file.

parseError(String) - Static method in class org.intermine.webservice.client.util.ErrorMessageParser

Parses service error message.

parseFacets(BrowseResult, Vector<KeywordSearchFacetData>, Map<String, String>) - Static method in class org.intermine.api.lucene.KeywordSearch

parseFileNames(File[]) - Method in class org.intermine.bio.dataconversion.UniprotConverter

sprot data files need to be processed immediately before trembl ones not all organisms are going to have both files UniProtFilterTask has already been run so all files are assumed to be valid.

parseFormatFromPathInfo(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser

Parse a format from the path-info of the request.

parseList(ServiceFactory, JSONObject) - Static method in class org.intermine.webservice.client.lists.Lists

Parse a list from its representation in JSON.

parseListCreationInfo(ServiceFactory, String) - Static method in class org.intermine.webservice.client.lists.Lists

Construct a representation of a list from the data returned by a call to create a new list.

parseParameterMap(String) - Static method in class org.intermine.webservice.client.util.URLParser

Returns parameters of URL as parameter map where key in the map is the parameter name and value is list of parameter values.

parser - Variable in class org.intermine.bio.task.GFF3ConverterTask

parseRange(String) - Method in class org.intermine.api.query.range.AbstractHelper

Construct a Range object from a string defining one of the ranges this constraint operates on.

parseRequest(HttpServletRequest, WebServiceInput) - Method in class org.intermine.webservice.server.WebServiceRequestParser

Parses common parameters for all web services.

parseResults(InterMineAPI, WebConfig, Collection<KeywordSearchHit>) - Static method in class org.intermine.web.search.SearchUtils

Parse the results into a human friendly form

parseServiceUrl(String) - Static method in class org.intermine.webservice.client.util.URLParser

Returns service URL - i.e.

parseTabDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser

Return an Iterator over a tab delimited file.

parseValue(String, Class<?>, ActionMessages) - Static method in class org.intermine.web.struts.QueryBuilderConstraintForm

Parse an attribute value

ParseValueException - Exception in org.intermine.pathquery

Exception thrown during parsing constraint value.

ParseValueException(String) - Constructor for exception org.intermine.pathquery.ParseValueException

Constructor

ParseValueException(String, Throwable) - Constructor for exception org.intermine.pathquery.ParseValueException

Constructor.

PartnerLink - Class in org.intermine.api.beans

A bean that contains the information to define a matching set of objects.

PartnerLink() - Constructor for class org.intermine.api.beans.PartnerLink

PartnerLinkBeanInfo - Class in org.intermine.api.beans

An object that describes the PartnerLink bean and supports DWR serialization.

PartnerLinkBeanInfo() - Constructor for class org.intermine.api.beans.PartnerLinkBeanInfo

password - Variable in class org.intermine.api.profile.Profile

password - Variable in class org.intermine.web.struts.CreateAccountForm

password - Variable in class org.intermine.web.struts.LoginForm

password - Variable in class org.intermine.web.struts.RequestPasswordForm

password2 - Variable in class org.intermine.web.struts.CreateAccountForm

PasswordHasher - Class in org.intermine.util

Utility methods for managing hashed passwords

PasswordResetAction - Class in org.intermine.web.struts

Action to change a user's password with the authority of a token previously emailed to them.

PasswordResetAction() - Constructor for class org.intermine.web.struts.PasswordResetAction

PasswordResetController - Class in org.intermine.web.struts

Controller for the password reset page.

PasswordResetController() - Constructor for class org.intermine.web.struts.PasswordResetController

PasswordResetForm - Class in org.intermine.web.struts

The form for resetting a password.

PasswordResetForm() - Constructor for class org.intermine.web.struts.PasswordResetForm

Path - Class in org.intermine.pathquery

Object to represent a path through an InterMine model.

Path(Model, String) - Constructor for class org.intermine.pathquery.Path

Create a new Path object.

Path(Model, String, Map<String, String>) - Constructor for class org.intermine.pathquery.Path

Create a Path object using class constraints from a Map.

path - Variable in class org.intermine.pathquery.PathConstraint

path - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

PATH_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

PathConstraint - Class in org.intermine.pathquery

Representation of a constraint in the PathQuery.

PathConstraint(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraint

Constructs a new PathConstraint.

PathConstraintAttribute - Class in org.intermine.pathquery

Representation of a normal attribute constraint in the PathQuery

PathConstraintAttribute(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintAttribute

Constructs a new PathConstraintAttribute.

PathConstraintBag - Class in org.intermine.pathquery

Representation of a constraint to a bag in the PathQuery

PathConstraintBag(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintBag

Constructs a new PathConstraintBag.

PathConstraintIds - Class in org.intermine.pathquery

Representation of a constraint to a collection of object ids in a query.

PathConstraintIds(String, ConstraintOp, Collection<Integer>) - Constructor for class org.intermine.pathquery.PathConstraintIds

Constructs a new PathConstraintIds.

PathConstraintLookup - Class in org.intermine.pathquery

Representation of a lookup constraint in the PathQuery

PathConstraintLookup(String, String, String) - Constructor for class org.intermine.pathquery.PathConstraintLookup

Constructs a new PathConstraintLookup.

PathConstraintLoop - Class in org.intermine.pathquery

Representation of a loop constraint in the PathQuery

PathConstraintLoop(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintLoop

Constructs a new PathConstraintLoop from one path to another.

PathConstraintMultitype - Class in org.intermine.pathquery

A constraint that restricts a path to inhabiting one of a list of types.

PathConstraintMultitype(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultitype

Construct a multi-type constraint.

PathConstraintMultiValue - Class in org.intermine.pathquery

Representation of a constraint to a collection of values in a query.

PathConstraintMultiValue(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultiValue

Constructs a new PathConstraintMultiValue.

PathConstraintNull - Class in org.intermine.pathquery

Representation of a null attribute constraint in the PathQuery

PathConstraintNull(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraintNull

Constructs a new PathConstraintNull.

PathConstraintRange - Class in org.intermine.pathquery

A constraint that restrict a path to a particular relationship with a set of ranges.

PathConstraintRange(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintRange

Constructs a new PathConstraintRange.

PathConstraintSubclass - Class in org.intermine.pathquery

Representation of a subclass constraint in the PathQuery.

PathConstraintSubclass(String, String) - Constructor for class org.intermine.pathquery.PathConstraintSubclass

Constructs a new PathConstraintSubclass.

PathException - Exception in org.intermine.pathquery

An Exception thrown if there is a problem in the Path class.

PathException(String, String) - Constructor for exception org.intermine.pathquery.PathException

Create a new PathException with the given message.

PathExpressionField - Class in org.intermine.objectstore.query

An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a part of the SELECT list of a QueryObjectPathExpression in single-row mode.

PathExpressionField(QueryObjectPathExpression, int) - Constructor for class org.intermine.objectstore.query.PathExpressionField

Constructor.

PathLengthComparator - Class in org.intermine.pathquery

PathLengthComparator() - Constructor for class org.intermine.pathquery.PathLengthComparator

protected constructor

pathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate

PathQuery - Class in org.intermine.pathquery

Class to represent a path-based query.

PathQuery(Model) - Constructor for class org.intermine.pathquery.PathQuery

Constructor.

PathQuery(PathQuery) - Constructor for class org.intermine.pathquery.PathQuery

Constructor.

PathQueryAPI - Class in org.intermine.api.query

Provides methods to obtain PathQueryExecutors and WebResultsExecutors

PathQueryBinding - Class in org.intermine.pathquery

Convert PathQueries to and from XML

PathQueryBinding() - Constructor for class org.intermine.pathquery.PathQueryBinding

PathQueryBuilder - Class in org.intermine.webservice.server.query.result

PathQueryBuilder builds PathQuery object from xml and validates it.

PathQueryBuilder(String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilder

PathQueryBuilder constructor.

PathQueryBuilderForJSONObj - Class in org.intermine.webservice.server.query.result

PathQueryBuilderForJSONObj() - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj

Constructor.

PathQueryBuilderForJSONObj(String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj

Constructor

PathQueryExecutor - Class in org.intermine.api.query

Executes path query and returns results in form suitable for export or web services.

PathQueryExecutor(ObjectStore, Profile, BagQueryRunner, BagManager) - Constructor for class org.intermine.api.query.PathQueryExecutor

Constructor with necessary objects.

pathQueryFormat - Variable in class org.intermine.api.profile.ProfileManager

Number determining format of queries in the database

PathQueryHandler - Class in org.intermine.pathquery

Extension of DefaultHandler to handle parsing PathQuery objects

PathQueryHandler(Map<String, PathQuery>, int) - Constructor for class org.intermine.pathquery.PathQueryHandler

Constructor

PathQueryHandler(Map<String, PathQuery>, int, Model) - Constructor for class org.intermine.pathquery.PathQueryHandler

Constructor.

pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction

Utility function to determine whether the PathQuery is publicly accessible.

pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.webservice.server.query.CodeService

Utility function to determine whether the PathQuery is publicly accessible.

PathQueryResultHelper - Class in org.intermine.web.logic.pathqueryresult

Helper for everything related to PathQueryResults

PathQueryUpdate - Class in org.intermine.api.profile

Class for updating a pathquery with a new model

PathQueryUpdate() - Constructor for class org.intermine.api.profile.PathQueryUpdate

Default constructor

PathQueryUpdate(PathQuery, Model) - Constructor for class org.intermine.api.profile.PathQueryUpdate

Construct with pathquery and former model

pathToIndex - Variable in class org.intermine.api.results.WebResults

PathUtil - Class in org.intermine.api.util

Utility methods for Paths

pathwayIdentifiers - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter

pathwaysNotStored - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter

pathWithNoConstraints(String) - Method in class org.intermine.web.logic.widget.TableWidgetLdr

PdbConverter - Class in org.intermine.bio.dataconversion

PdbConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PdbConverter

Create a new PdbConverter object.

pending - Static variable in class org.intermine.objectstore.query.PrefetchManager

Pending set of requests - always accessed inside a synchronise on sync.

PendingClob - Class in org.intermine.objectstore.query

Subclass of ClobAccess that contains data to be written to the database instead of access to data already in the database.

PendingClob(String) - Constructor for class org.intermine.objectstore.query.PendingClob

Construct a PendingClob from a String.

PER_PAGE - Static variable in class org.intermine.api.lucene.KeywordSearch

maximum number of items to be displayed on a page

PerformanceTester - Class in org.intermine.web.commandline

Class to run a performance test on a production database by loading a set of template queries from a userprofile database and running them in varying numbers of threads.

performSearch(String, String) - Method in class org.intermine.web.autocompletion.LuceneSearchEngine

Perform the lucene search.

performUnsafeOperation(String, SQLOperation<T>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Convenience wrapper to manage the boilerplate when performing unsafe operations.

perm - Variable in class org.intermine.task.GrantTask

PermaTokenDeletionService - Class in org.intermine.webservice.server.user

Does what it says on the tin.

PermaTokenDeletionService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenDeletionService

Constructor.

PermaTokenInfoService - Class in org.intermine.webservice.server.user

PermaTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenInfoService

PermaTokens - Class in org.intermine.webservice.server.user

PermaTokensServlet - Class in org.intermine.webservice.server.user

PermaTokensServlet() - Constructor for class org.intermine.webservice.server.user.PermaTokensServlet

pilferObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Gets a object from the cache if it is present.

pilferObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore

Gets a object from the cache if it is present.

pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Gets a object from the cache if it is present.

pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Gets a object from the cache if it is present.

pkQueryFruitless(Class<? extends FastPathObject>, String, Object) - Method in class org.intermine.dataloader.EquivalentObjectHints

Returns true if there were no instances of the given class with the given field set to the given value.

PkQueryIdUpgrader - Class in org.intermine.web.bag

Bag object id upgrader that uses the primary keys to find the objects in the new ObjectStore.

PkQueryIdUpgrader(ObjectStore) - Constructor for class org.intermine.web.bag.PkQueryIdUpgrader

No argument constructor - will use all available keyDefs to upgrade bags.

PkQueryIdUpgrader(String, ObjectStore) - Constructor for class org.intermine.web.bag.PkQueryIdUpgrader

Construct with the name of a source - will use defined keys to upgrade bags.

PLAIN_TEXT - Static variable in class org.intermine.webservice.server.lists.ListUploadService

PlainFormatter - Class in org.intermine.webservice.server.output

Simplest possible formatting.

PlainFormatter() - Constructor for class org.intermine.webservice.server.output.PlainFormatter

platform - Variable in class org.intermine.sql.Database

PLUS - Static variable in class org.intermine.sql.query.Function

PLUS function - takes two or more operands.

POLL_REFRESH_SECONDS - Static variable in class org.intermine.web.logic.Constants

Refresh period specified on query poll page.

PollQueryAction - Class in org.intermine.web.struts

Repeatedly poll the status of a running query and forward client to appropriate page each time.

PollQueryAction() - Constructor for class org.intermine.web.struts.PollQueryAction

popTag() - Method in class org.intermine.webservice.server.output.XMLFormatter

Say that we are finished with the current tag.

PopulateChildFeatures - Class in org.intermine.bio.postprocess

Populate the SequenceFeature.childFeatures() collection for: Gene, Transcript, Exon Only used for JBrowse

PopulateChildFeatures(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.PopulateChildFeatures

Construct with an ObjectStoreWriter, read and write from same ObjectStore

populateCollection() - Method in class org.intermine.bio.postprocess.PopulateChildFeatures

Populate the SequenceFeature.locatedFeatures() collection for: Gene, Transcript, Exon and CDS

populateFromFile(File) - Method in class org.intermine.bio.dataconversion.IdResolver

Read contents of an IdResolver from file, allows for caching during a build.

populateIds(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Populates the object o with IDs.

populateList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput

read the parameters into a list.

populateListMap(Map<String, InterMineBag>, String) - Method in class org.intermine.webservice.server.lists.ListInput

Fill a map with intermine bags from the names in a parameter.

populateNormedList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput

Read parameters into a list, normalising the values.

populateObject(Item, Map<String, FastPathObject>, boolean, boolean, FastPathObject) - Static method in class org.intermine.xml.full.FullParser

Fill in fields of an outline business object which is in the map under item.identifier Note that this modifies the relevant object in the map It also returns the object for convenience

populateRequest(HttpServletRequest, HttpServletResponse) - Static method in class org.intermine.web.struts.QueryBuilderController

Populate the request with the necessary attributes to render the query builder page.

populateSearchItems() - Method in class org.intermine.api.search.GlobalRepository

populateSearchItems() - Method in class org.intermine.api.search.SearchRepository

Collect the search items we are interested in initially.

populateSearchItems() - Method in class org.intermine.api.search.UserRepository

populateSOTermMap(ObjectStore) - Method in class org.intermine.bio.postprocess.PopulateChildFeatures

populateTemplateOneConstraint(TemplateQuery, ConstraintOp, String) - Static method in class org.intermine.api.template.TemplatePopulator

Populate a TemplateQuery that has a single editable constraint with the given value.

populateTemplateWithBag(TemplateQuery, InterMineBag) - Static method in class org.intermine.api.template.TemplatePopulator

Constrain a template query with a single editable constraint to be in the given bag.

populateTemplateWithObject(TemplateQuery, InterMineObject) - Static method in class org.intermine.api.template.TemplatePopulator

Constrain a template query with a single editable constraint to be the given object.

populationBagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

PopulationInfo - Class in org.intermine.web.logic.widget

Container for size and extra attribute (e.g. gene length average) for the whole population

PopulationInfo(int, float) - Constructor for class org.intermine.web.logic.widget.PopulationInfo

Constructor

PORTAL_MSG - Static variable in class org.intermine.web.logic.Constants

Session attribute that temporarily holds messages from the Portal

PortalHelper - Class in org.intermine.web.logic

Util methods for the portal

PortalQueryAction - Class in org.intermine.web.struts

The portal query action handles links into flymine from external sites.

PortalQueryAction() - Constructor for class org.intermine.web.struts.PortalQueryAction

possibleValues - Variable in class org.intermine.api.template.TemplateSummariser

PossibleValuesService - Class in org.intermine.webservice.server.path

A service for retrieving the possible values for a path in the data model.

PossibleValuesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.path.PossibleValuesService

A service for providing column summary information.

PossibleValuesServlet - Class in org.intermine.webservice.server.path

A servlet for routing requests to the possible values service.

PossibleValuesServlet() - Constructor for class org.intermine.webservice.server.path.PossibleValuesServlet

Constructor.

postDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

PostgresByteArrayOutputStream - Class in org.intermine.sql.writebatch

A subclass of SensibleByteArrayOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.

PostgresByteArrayOutputStream() - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream

PostgresByteArrayOutputStream(int) - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream

PostgresDataOutputStream - Class in org.intermine.sql.writebatch

A subclass of DataOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.

PostgresDataOutputStream(OutputStream) - Constructor for class org.intermine.sql.writebatch.PostgresDataOutputStream

PostgresExplainResult - Class in org.intermine.sql.query

Subclass of ExplainResult specific to PostgreSQL.

PostgresExplainResult() - Constructor for class org.intermine.sql.query.PostgresExplainResult

Constructs an instance of PostgresExplainResult without any data.

PostgresExplainResult(Query, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult

Constructs an instance of PostgresExplainResult for a given Query and database Connection.

PostgresExplainResult(String, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult

Constructs an instance of PostgresExplainResult for a given Query String and database Connection.

PostgresExplainResult(PreparedStatement) - Constructor for class org.intermine.sql.query.PostgresExplainResult

Constructs an instance of ExplainResult given a PreparedStatement object.

postInit() - Method in class org.intermine.webservice.server.core.JSONService

postInit() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService

postInit() - Method in class org.intermine.webservice.server.path.PossibleValuesService

postInit() - Method in class org.intermine.webservice.server.query.QueryRetrieverService

postInit() - Method in class org.intermine.webservice.server.query.QueryUploadService

postInit() - Method in class org.intermine.webservice.server.query.result.QueryResultService

postInit() - Method in class org.intermine.webservice.server.WebService

Subclasses can hook in here to do common behaviour that needs to happen after initialisation.

postProcess() - Method in class org.intermine.bio.postprocess.FlyBasePostProcess

All subclasses should override this method so they can be called in a generic fashion.

postProcess() - Method in class org.intermine.bio.postprocess.GoPostprocess

Copy all GO annotations from the Protein objects to the corresponding Gene(s)

postProcess() - Method in class org.intermine.postprocess.PostProcessor

All subclasses should override this method so they can be called in a generic fashion.

PostProcessOperationsTask - Class in org.intermine.bio.postprocess

Run operations on genomic model database after DataLoading

PostProcessOperationsTask() - Constructor for class org.intermine.bio.postprocess.PostProcessOperationsTask

PostProcessor - Class in org.intermine.postprocess

Generic defn of a post process step...

PostProcessor(ObjectStoreWriter) - Constructor for class org.intermine.postprocess.PostProcessor

Typical constructor with a handle to the object store we are working on.

PostProcessorTask - Class in org.intermine.task

Generic defn of a post process step...

PostProcessorTask() - Constructor for class org.intermine.task.PostProcessorTask

PostProcessUtil - Class in org.intermine.bio.postprocess

Common operations for post processing.

POWER - Static variable in class org.intermine.sql.query.Function

POWER function - takes two operands.

PQUtil - Class in org.intermine.webservice.client.util

Static methods to make certain path-query based operations easier.

preCompute(String) - Method in class org.intermine.dwr.AjaxServices

Precomputes the given template query

precompute(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates precomputed tables for the given query.

precompute(Query, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates precomputed tables for the given query.

precompute(Query, Collection<? extends QueryNode>, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates precomputed tables for the given query.

precompute(Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates precomputed tables for the given query.

precompute(Collection<ParallelPrecomputer.Job>) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer

Perform a load of precompute operations in parallel.

precompute(boolean, ObjectStore, int) - Method in class org.intermine.task.PrecomputeTask

Create precomputed tables for the given ObjectStore.

precompute(Query, Collection<QueryNode>, String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Call ObjectStoreInterMineImpl.precompute() with the given Query.

PRECOMPUTE_CATEGORY - Static variable in class org.intermine.bio.util.Constants

The category to pass to ObjectStoreInterMineImpl.precompute().

PRECOMPUTE_CATEGORY_TEMPLATE - Static variable in class org.intermine.web.task.PrecomputeTemplatesTask

The precompute category to use for templates.

PrecomputedTable - Class in org.intermine.sql.precompute

Represents a Precomputed table in a database.

PrecomputedTable(Query, String, String, String, Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTable

Construct a new PrecomputedTable

PrecomputedTableManager - Class in org.intermine.sql.precompute

Manages all the Precomputed tables in a given database.

PrecomputedTableManager(Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager

Create a PrecomputedTableManager for a given Connection.

PrecomputedTableManager(Database) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager

Create a PrecomputedTableManager for the given underlying database.

precomputedTables - Variable in class org.intermine.sql.precompute.PrecomputedTableManager

precomputeQuery(String, Query, Collection<? extends QueryNode>, boolean, String, int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer

Call ObjectStoreInterMineImpl.precompute() with the given Query.

PrecomputeTask - Class in org.intermine.task

A Task that reads a list of queries from a properties file (eg. testmodel_precompute.properties) and calls ObjectStoreInterMineImpl.precompute() using the Query.

PrecomputeTask() - Constructor for class org.intermine.task.PrecomputeTask

precomputeTemplate(TemplateQuery) - Method in class org.intermine.api.query.WebResultsExecutor

Precomputes a template query if it is not already precomputed, returning whether precomputing was necessary.

precomputeTemplates() - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Create precomputed tables for all template queries in the given ObjectStore.

PrecomputeTemplatesTask - Class in org.intermine.web.task

A Task that reads a list of queries from a properties file (eg. testmodel_precompute.properties) and calls ObjectStoreInterMineImpl.precompute() using the Query.

PrecomputeTemplatesTask() - Constructor for class org.intermine.web.task.PrecomputeTemplatesTask

precomputeWithConnection(Connection, Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Creates precomputed tables with the given query and connection.

preDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Predicate<T> - Interface in org.intermine.webservice.server.core

The type of functions that test things.

PreferencesHandler - Class in org.intermine.api.profile

PreferencesHandler(Map<String, String>) - Constructor for class org.intermine.api.profile.PreferencesHandler

PreferencesManager - Class in org.intermine.api.profile

Class encapsulating the logic for reading user preferences in and out of the DB.

PreferencesManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.PreferencesManager

Constructor

prefers(String) - Method in class org.intermine.api.profile.Profile

Determine whether a user perfers a certain thing or not.

prefetch - Variable in class org.intermine.objectstore.query.Results

prefetch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Prefetch into memory the batch indicated with the given batch number.

prefetchIds(Set<Integer>) - Method in class org.intermine.dataloader.DataTracker

Prefetches data for a specified set of object ids.

PrefetchManager - Class in org.intermine.objectstore.query

A manager for the prefetch mechanism for the Results object.

prefetchObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Prefetches an object into the objectstore getObjectById cache.

prefetchObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore

Prefetches an object into the objectstore getObjectById cache.

prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl

Prefetches an object into the objectstore getObjectById cache.

prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl

Prefetches an object into the objectstore getObjectById cache.

prefix - Variable in class org.intermine.bio.dataconversion.OboConverter

PREV_TEMPLATE_NAME - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the previous template name

previousPage() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Go to the previous page

println() - Method in class org.intermine.web.logic.export.CustomPrintWriter

printStyleAndClass(JspWriter) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Prints 'style' and 'class' attributes of element.

priorityConfig - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

PriorityConfig - Class in org.intermine.dataloader

Class holding data source priority configuration for a Model.

PriorityConfig(Model) - Constructor for class org.intermine.dataloader.PriorityConfig

Constructor.

PRIVATEKEY_ALIAS - Static variable in class org.intermine.web.task.IssueTokenTask

The alias of the private key

PRIVATEKEY_PASSWORD - Static variable in class org.intermine.web.task.IssueTokenTask

The password of the private key.

process(Reader) - Method in class org.intermine.bio.dataconversion.BioGridConverter

Perform the currentFile conversion

process() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Process the data from the Database and write to the ItemWriter.

process(Connection) - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Do the processing for this module - called by ChadoDBConverter.

process() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Process and load all of the fasta files.

process(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3Converter

process GFF3 record and give a xml presentation

process(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Method to perform additional operations for a GFF3Record.

process(Reader) - Method in class org.intermine.bio.dataconversion.GoConverter

Perform the currentFile conversion

process(Reader) - Method in class org.intermine.bio.dataconversion.InterProConverter

Perform the currentFile conversion

process(Reader) - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter

Read each line from flat file, create genes and synonyms.

process(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

Do the processing for this module - called by ChadoDBConverter.

process() - Method in class org.intermine.bio.dataconversion.OboConverter

Process every DAG term and output it as a Item.

process(OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter

Convert a OboTerm into an Item and relation Items, and write the relations to the writer.

process(File) - Method in class org.intermine.bio.dataconversion.PdbConverter

Perform the conversion files in the directory

process(Reader) - Method in class org.intermine.bio.dataconversion.PsiConverter

Perform the currentFile conversion

process(Reader) - Method in class org.intermine.bio.dataconversion.PubMedGeneConverter

Process references file and gene information file.

process(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Do the processing for this module - called by ChadoDBConverter.

process(Connection) - Method in class org.intermine.bio.dataconversion.StockProcessor

Do the processing for this module - called by ChadoDBConverter.

process(File) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Perform the conversion files in the directory

process(Reader) - Method in class org.intermine.bio.dataconversion.UniprotKeywordConverter

Perform the currentFile conversion

process() - Method in class org.intermine.codegen.JavaModelOutput

Perform the mapping.

process() - Method in class org.intermine.dataconversion.DBConverter

Query from database and write items to the writer.

process(File) - Method in class org.intermine.dataconversion.DirectoryConverter

Perform the conversion files in the directory

process(Reader) - Method in class org.intermine.dataconversion.FileConverter

Perform the currentFile conversion

process(Reader) - Method in class org.intermine.dataconversion.FullXmlConverter

Unmarshal the Items from the input XML file, and write them to the writer.

process(ObjectStore, Source, Source) - Method in class org.intermine.dataloader.ObjectStoreDataLoader

Performs the loading operation, reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.

process(ObjectStore, Source, Source, Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.ObjectStoreDataLoader

Loads only a specified class reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.

process() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput

Process the schema and put the output in the file.

process() - Method in class org.intermine.task.DirectDataLoaderTask

Called by execute() to process the data.

process() - Method in class org.intermine.task.FileDirectDataLoaderTask

process() - Method in class org.intermine.web.logic.widget.EnrichmentWidget

process() - Method in class org.intermine.web.logic.widget.GraphWidget

Process the data and create the widget

process() - Method in class org.intermine.web.logic.widget.HTMLWidget

process() - Method in class org.intermine.web.logic.widget.TableWidget

Process the data and create the widget

process() - Method in class org.intermine.web.logic.widget.Widget

Process the data and create the widget

process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.FlatWidgetProcessor

process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.JSONWidgetProcessor

process(String, WidgetConfig) - Method in interface org.intermine.webservice.server.widget.WidgetProcessor

Process a widget.

process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl

Process a list called x with a widget y

process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.XMLWidgetProcessor

processConstraint(PathQuery, String, Map<String, String>, Collection<String>) - Method in class org.intermine.pathquery.PathQueryHandler

Process a constraint from the xml attributes.

processFile(File) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Handles each fasta file.

processFile(File) - Method in class org.intermine.task.FileDirectDataLoaderTask

Called by process() once for each File we need to process.

processFile(File) - Method in class org.intermine.task.TSVFileReaderTask

Query all objects of the class given by the className specified in the configurationFile.

processForwardConfig(HttpServletRequest, HttpServletResponse, ForwardConfig) - Method in class org.intermine.web.struts.InterMineRequestProcessor

Overridden to copy errors and messages to session before performing a redirecting forward.

processGroupClause(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a GROUP clause.

processIdentifiers(String, ListCreationInput, Set<String>, Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListUploadService

Process the identifiers.

processing() - Method in class org.intermine.bio.dataconversion.UniprotEntry

this check is necessary because the xml attributes may occur in other XML entries

processingFeature() - Method in class org.intermine.bio.dataconversion.UniprotEntry

this check is necessary because the xml attributes may occur in other XML entries.

processItem(DataConverter, Item) - Method in class org.intermine.bio.dataconversion.BioStoreHook

Assigns SO terms and datasets to item, if appropriate.

processItem(DataConverter, Item) - Method in interface org.intermine.dataconversion.DataConverterStoreHook

This method is called before storing an Item.

processLimitClause(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a Limit clause.

processLocationTable(Connection, ResultSet) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Process a featureloc table and create Location objects.

processNewAbstractConstraint(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes an AbstractConstraint.

processNewAbstractValue(AST) - Method in class org.intermine.sql.query.Query

Processes a single AST node that describes an AbstractValue.

processNewField(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a Field.

processNewSafeFunction(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a safe function.

processNewSelect(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a SelectValue.

processNewTypecast(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a typecast.

processNewUnsafeFunction(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes an unsafe function.

processOntology(Reader) - Method in class org.intermine.bio.ontology.OboParser

Parse an OBO file to produce a set of OboTerms.

processOrderClause(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a ORDER clause.

processPreprocess(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineRequestProcessor

This is called during the processing of every controller.

processQuery(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj

Transform a query from a standard one into one that conforms to the requirements of JSON objects.

processRelation(OboRelation) - Method in class org.intermine.bio.dataconversion.OboConverter

Process and store OboRelations

processRelations(String) - Method in class org.intermine.bio.ontology.OboParser

Parse the relations file generated by the OboEdit reasoner (calculates transitivity)

processResults(List<AcceptanceTestResult>, PrintWriter) - Method in class org.intermine.task.AcceptanceTestTask

Write a formatted HTML summary of the given AcceptanceTestResult objects to the PrintWriter.

processSelectList(AST) - Method in class org.intermine.sql.query.Query

Processes an AST node that describes a SELECT list.

processValue(String) - Method in class org.intermine.bio.chado.config.MatchingFieldConfigAction

Process the value to set and return a (possibly) altered version.

processXml(InputStream, Source, Source) - Method in class org.intermine.dataloader.XmlDataLoader

Static method to unmarshall business objects from a given xml file and call store on each.

produce() - Method in class org.intermine.webservice.server.core.ListManager

produce() - Method in interface org.intermine.webservice.server.core.Producer

produceName() - Method in class org.intermine.webservice.server.lists.ListInput

produceName() - Method in class org.intermine.webservice.server.lists.ListRenameInput

Producer<T> - Interface in org.intermine.webservice.server.core

The type of functions that take no input and produce a value.

productMap - Variable in class org.intermine.bio.dataconversion.GoConverter

Profile - Class in org.intermine.api.profile

Class to represent a user of the webapp The profile is responsible for informing its search repository of all web-searchable objects created or deleted on its watch.

Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile

Construct a Profile

Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile

Construct a Profile

Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, BagSet, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile

Construct a Profile

Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile

Construct a profile without an API key

profile - Variable in class org.intermine.api.query.QueryExecutor

The profile to use to find bags from.

profile - Variable in class org.intermine.api.search.SearchRepository

PROFILE - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the user's Profile

profile - Variable in class org.intermine.webservice.server.lists.ListInput

profile - Variable in class org.intermine.webservice.server.query.QueryUploadService

PROFILE_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store profile format version.

ProfileAlreadyExistsException - Exception in org.intermine.api.profile

Exception thrown when attempting to create a profile element with a name that already exists.

ProfileAlreadyExistsException(String) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException

Constructs an ProfileNameAlreadyExistsExceptionException with the specified detail message.

ProfileAlreadyExistsException(Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException

Constructs an ProfileAlreadyExistsExceptionException with the specified nested throwable.

ProfileAlreadyExistsException(String, Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException

Constructs an ProfileAlreadyExistsExceptionException with the specified detail message and nested throwable.

ProfileBinding - Class in org.intermine.api.xml

Code for reading and writing Profile objects as XML.

profileCache - Variable in class org.intermine.api.profile.ProfileManager

profileId - Variable in class org.intermine.api.profile.StorableBag

profileManager - Variable in class org.intermine.api.bag.SharedBagManager

profileManager - Variable in class org.intermine.api.InterMineAPI

ProfileManager - Class in org.intermine.api.profile

Class to manage and persist user profile data such as saved bags

ProfileManager(ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.ProfileManager

Construct a ProfileManager for the webapp

ProfileManager.ApiPermission - Class in org.intermine.api.profile

A representation of the level of permissions granted to a user.

ProfileManager.ApiPermission.Level - Enum in org.intermine.api.profile

The possible permission levels.

ProfileManager.AuthenticationException - Exception in org.intermine.api.profile

Exception thrown when the authentication fails.

ProfileManager.AuthenticationException(String) - Constructor for exception org.intermine.api.profile.ProfileManager.AuthenticationException

Constructor

ProfileManagerBinding - Class in org.intermine.api.xml

Code for reading and writing ProfileManager objects as XML

ProfileMergeIssues - Class in org.intermine.web.logic.profile

The problems that arose when merging two profiles.

ProfileMergeIssues() - Constructor for class org.intermine.web.logic.profile.ProfileMergeIssues

ProfileReadTask - Class in org.intermine.web.task

Task to read an XML file of a webapp userprofiles into a userprofile ObjectStore.

ProfileReadTask() - Constructor for class org.intermine.web.task.ProfileReadTask

ProfileWriteTask - Class in org.intermine.web.task

Task to write an XML file of a webapp userprofile object store.

ProfileWriteTask() - Constructor for class org.intermine.web.task.ProfileWriteTask

PROP_FILE - Static variable in class org.intermine.bio.dataconversion.GFF3Converter

PROP_FILE - Static variable in class org.intermine.bio.dataconversion.GoConverter

PROPERTIES_ORIGINS - Static variable in class org.intermine.web.logic.Constants

Attribute used to store origin information about properties in the context of this web application.

PropertiesUtil - Class in org.intermine.util

Convenience class for working with global properties

PropertyChangeEvent - Class in org.intermine.api.search

A representation of a notification that a property of a web searchable has changed.

PropertyChangeEvent(WebSearchable) - Constructor for class org.intermine.api.search.PropertyChangeEvent

Constructor.

PROVIDER - Static variable in class org.intermine.web.logic.Constants

The name of the current open-id provider

ProxyCollection<E> - Class in org.intermine.objectstore.proxy

Class which holds a reference to a collection in the database

ProxyCollection(ObjectStore, InterMineObject, String, Class<? extends E>) - Constructor for class org.intermine.objectstore.proxy.ProxyCollection

Construct a ProxyCollection object.

ProxyReference - Class in org.intermine.objectstore.proxy

Class which holds a reference to an object in the database

ProxyReference(ObjectStore, Integer, Class<? extends InterMineObject>) - Constructor for class org.intermine.objectstore.proxy.ProxyReference

Construct a ProxyReference object.

PseudoSet<E> - Class in org.intermine.util

A Set that does not actually contain objects, but provides useful results for the contains method.

PseudoSet() - Constructor for class org.intermine.util.PseudoSet

PsiConverter - Class in org.intermine.bio.dataconversion

DataConverter to parse psi data into items Experiments and interactions appear in different files, so we have to keep all experiments until all interactions are processed.

PsiConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PsiConverter

Constructor

PUBLIC_TAG_LIST - Static variable in class org.intermine.web.struts.InitialiserPlugin

The list of tags that mark something as public

PUBLICIDENTITY - Static variable in class org.intermine.web.task.IssueTokenTask

The identity of the issuing entity (i.e. us)

PublicKeySource - Interface in org.intermine.web.security

An object that can provide public keys by name, or all known keys, or a subset of keys.

PubMedGeneConverter - Class in org.intermine.bio.dataconversion

DataConverter creating items from PubMed data file

PubMedGeneConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PubMedGeneConverter

pubRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

pureObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

This is a list of the objects that did not merge with anything from a previous data source

pushTag(String) - Method in class org.intermine.webservice.server.output.XMLFormatter

Set the current tag we are working within.

put(String, String) - Method in class org.intermine.api.profile.UserPreferences

put(K, V) - Method in class org.intermine.api.util.DevNullMap

put(String, Source) - Method in class org.intermine.dataloader.ObjectDescription

Adds a fieldname-source mapping for this ObjectDescription that is not present in the backing database.

put(K, V) - Method in class org.intermine.util.AlwaysMap

put(E, E) - Method in class org.intermine.util.IdentityMap

put(int, int) - Method in class org.intermine.util.IntToIntMap

Creates a mapping in the object.

put(Integer, Integer) - Method in class org.intermine.util.IntToIntMap

Puts a mapping in the object.

put(E) - Method in class org.intermine.util.ObjectPipe

Adds an Object onto the end of the queue.

put(K, V) - Method in class org.intermine.util.ReferenceMap

put(InterMineObject, ReportObject) - Method in class org.intermine.web.logic.results.ReportObjectFactory

Disable this method.

putAll(Map<? extends String, ? extends String>) - Method in class org.intermine.api.profile.UserPreferences

putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.AlwaysMap

putAll(Map<? extends E, ? extends E>) - Method in class org.intermine.util.IdentityMap

putAll(Collection<? extends E>) - Method in class org.intermine.util.ObjectPipe

Adds a whole Collection of Objects onto the end of the queue, in the order that the Collection's Iterator presents them.

putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.ReferenceMap

putClean(String, Source) - Method in class org.intermine.dataloader.ObjectDescription

Adds a fieldname-source mapping for this ObjectDescription while keeping it clean.

putQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore

putQuery(String) - Method in interface org.intermine.api.query.QueryStore

Q

q - Variable in class org.intermine.sql.precompute.PrecomputedTable

qc - Variable in class org.intermine.objectstore.query.QueryForeignKey

qc - Variable in class org.intermine.objectstore.query.QueryReference

qc1 - Variable in class org.intermine.objectstore.query.ClassConstraint

qc2 - Variable in class org.intermine.objectstore.query.ClassConstraint

qcb - Variable in class org.intermine.objectstore.query.QueryCollectionReference

qcObj - Variable in class org.intermine.objectstore.query.QueryCollectionReference

qe - Variable in class org.intermine.objectstore.query.SubqueryConstraint

qe1 - Variable in class org.intermine.objectstore.query.SimpleConstraint

qe2 - Variable in class org.intermine.objectstore.query.SimpleConstraint

qn - Variable in class org.intermine.objectstore.query.BagConstraint

queries - Variable in class org.intermine.sql.precompute.BestQueryStorer

QUERIES_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService

The key for the queries parameter

queriesInUnion - Variable in class org.intermine.sql.query.Query

Query - Class in org.intermine.objectstore.query

This class provides an implementation-independent abstract representation of a query

Query() - Constructor for class org.intermine.objectstore.query.Query

Empty constructor.

query - Variable in class org.intermine.objectstore.query.ResultsBatches

query - Variable in class org.intermine.pathquery.PathQueryHandler

query - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

query - Variable in class org.intermine.sql.precompute.BestQueryFallback

Query - Class in org.intermine.sql.query

Represents an SQL query in parsed form.

Query() - Constructor for class org.intermine.sql.query.Query

Construct a new Query.

Query(Map<String, AbstractTable>) - Constructor for class org.intermine.sql.query.Query

Construct a new Query.

Query(Map<String, AbstractTable>, List<Query>) - Constructor for class org.intermine.sql.query.Query

Construct a new Query.

Query(String) - Constructor for class org.intermine.sql.query.Query

Construct a new parsed Query from a String.

Query(String, boolean) - Constructor for class org.intermine.sql.query.Query

Construct a new parsed Query from a String.

Query(String, Long) - Constructor for class org.intermine.sql.query.Query

Construct a new parsed Query from a String.

Query(String, boolean, Long) - Constructor for class org.intermine.sql.query.Query

Construct a new parsed Query from a String.

query - Variable in class org.intermine.sql.query.SubQuery

query - Variable in class org.intermine.task.RunIqlQueryTask

QUERY - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the current query

QUERY_FOR_GOFASTER - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

query for go faster

QUERY_FOR_PRECOMP - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

query for precomputing

QUERY_NORMAL - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

normal query

QUERY_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser

Name of parameter with query

QUERY_SUBQUERY_CONSTRAINT - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

subquery in CONSTRAINT

QUERY_SUBQUERY_EXISTS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

subquery exists

QUERY_SUBQUERY_FROM - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

subquery in FROM

QUERY_TIMEOUT_SECONDS - Static variable in class org.intermine.web.logic.Constants

Period of time to wait for client to poll a running query before cancelling the query.

QUERY_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of class that tracks queries

QUERY_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of table that tracks queries

Queryable - Interface in org.intermine.objectstore.query

An interface for an object that has a SELECT list and a WHERE clause, like a Query.

QueryBuilderChange - Class in org.intermine.web.struts

Action to handle links on main query builder tile.

QueryBuilderChange() - Constructor for class org.intermine.web.struts.QueryBuilderChange

QueryBuilderConstraintAction - Class in org.intermine.web.struts

Action to handle button presses on the main tile

QueryBuilderConstraintAction() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintAction

QueryBuilderConstraintController - Class in org.intermine.web.struts

Controller for the main constraint editing tile

QueryBuilderConstraintController() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintController

QueryBuilderConstraintForm - Class in org.intermine.web.struts

The form used for editing QueryBuilder constraints

QueryBuilderConstraintForm() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintForm

QueryBuilderController - Class in org.intermine.web.struts

Controller for the main query builder tile.

QueryBuilderController() - Constructor for class org.intermine.web.struts.QueryBuilderController

QueryBuilderSummaryController - Class in org.intermine.web.struts

Controller for the QueryBuilder summary tile.

QueryBuilderSummaryController() - Constructor for class org.intermine.web.struts.QueryBuilderSummaryController

QueryBuilderSummaryHelper - Class in org.intermine.web.logic.querybuilder

Methods to generate summary information for a PathQuery for use in display of QueryBuilder summary section.

QueryBuilderViewAction - Class in org.intermine.web.struts

Action to run constructed query.

QueryBuilderViewAction() - Constructor for class org.intermine.web.struts.QueryBuilderViewAction

QueryBuilderViewChange - Class in org.intermine.web.struts

Action to handle links on view tile

QueryBuilderViewChange() - Constructor for class org.intermine.web.struts.QueryBuilderViewChange

queryCancelled() - Method in interface org.intermine.web.logic.query.QueryMonitor

Called when the query is cancelled.

queryCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Called when the query is cancelled.

queryCancelledWithError() - Method in interface org.intermine.web.logic.query.QueryMonitor

Called when the query stopped with an error.

queryCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Called when the query stopped with an error.

QueryCast - Class in org.intermine.objectstore.query

Represents a type cast in a Query.

QueryCast(QueryEvaluable, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryCast

Construct a QueryCast.

queryClass - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

QueryClass - Class in org.intermine.objectstore.query

Represents the database extent of a Java class NOTE - No equals() method is defined for this class and none should be.

QueryClass(Class<? extends FastPathObject>) - Constructor for class org.intermine.objectstore.query.QueryClass

Constructs a QueryClass representing the specified Java class

QueryClass(Set<Class<?>>) - Constructor for class org.intermine.objectstore.query.QueryClass

Constructs a QueryClass representing the specified set of classes

QueryClass(Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryClass

Constructs a QueryClass representing the specified array of classes

QueryClassBag - Class in org.intermine.objectstore.query

An element that can appear in the FROM clause of a query

QueryClassBag(Class<? extends InterMineObject>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag

Constructs a QueryClassBag representing the specified Java class and bag of objects.

QueryClassBag(Set<Class<?>>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag

Constructs a QueryClass representing the specified set of classes and bag of objects.

QueryClassBag(Class<? extends InterMineObject>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag

Constructs a QueryClassBag representing the specified Java class and ObjectStoreBag.

QueryClassBag(Set<Class<?>>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag

Constructs a QueryClass representing the specified set of classes and ObjectStoreBag.

queryClassInQuery - Variable in class org.intermine.web.logic.widget.WidgetLdr

QueryClassSelectAction - Class in org.intermine.web.struts

Implementation of Action that processes QueryClass selection form.

QueryClassSelectAction() - Constructor for class org.intermine.web.struts.QueryClassSelectAction

QueryClassSelectForm - Class in org.intermine.web.struts

Form bean for selection of a new query class.

QueryClassSelectForm() - Constructor for class org.intermine.web.struts.QueryClassSelectForm

queryClassToString(StringBuffer, QueryClass, Query, DatabaseSchema, int, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a QueryClass to a String.

QueryCloner - Class in org.intermine.objectstore.query

This is a static class that provides a method to clone a Query object.

QueryCollectionPathExpression - Class in org.intermine.objectstore.query

An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a collection or reference referenced in an object in the results.

QueryCollectionPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression

Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name.

QueryCollectionPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression

Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name, constrained to be a particular subclass.

queryCollectionPathExpressionToString(Query, List<Object>, QueryCollectionPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts a QueryObjectPathExpression into a String.

QueryCollectionReference - Class in org.intermine.objectstore.query

Represents a field of a QueryClass that is a collection

QueryCollectionReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference

Constructs a QueryCollectionReference representing the specified field of a QueryClass

QueryCollectionReference(QueryClassBag, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference

Constructs a QueryCollectionReference representing the specified field of a QueryClassBag

QueryCollectionReference(InterMineObject, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference

Constructs a QueryCollectionReference representing the specified field of an object

queryCompleted() - Method in interface org.intermine.web.logic.query.QueryMonitor

Called when the query has completed.

queryCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Called when the query has completed.

QueryCountQueryMonitor - Class in org.intermine.web.logic.session

A QueryMonitor that maintains a timeout and is used when counting the number of rows a query returns.

QueryCountQueryMonitor(int, Query) - Constructor for class org.intermine.web.logic.session.QueryCountQueryMonitor

Construct a new instance of QueryCountQueryMonitor.

QueryCreator - Class in org.intermine.objectstore.query

Class that helps build queries or parts of queries for common situations.

queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher

Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BatchingFetcher

Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

queryEquivalentObjects(InterMineObject, Source) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher

Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.HintingFetcher

Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.

QueryEvaluable - Interface in org.intermine.objectstore.query

An element that can be evaluated for comparison (one that represents an atomic type)

queryEvaluableToString(StringBuffer, QueryEvaluable, Query, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a QueryEvaluable into a String suitable for an SQL query String.

QueryExecutor - Class in org.intermine.api.query

Common superclass of query executors that holds cache of pathToQueryNode maps per query.

QueryExecutor() - Constructor for class org.intermine.api.query.QueryExecutor

QueryExpression - Class in org.intermine.objectstore.query

Represents an arithmetic or substring expression, analogous to those in SQL

QueryExpression(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression

Constructs an arithmetic QueryExpression from two evaluable items

QueryExpression(QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression

Constructs a substring QueryExpression from a QueryEvaluable and start and length QueryEvaluables

QueryExpression(int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression

Constructs a String QueryExpression to perform upper and lowercase conversions.

queryExpressionToString(Query, QueryExpression, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts a QueryExpression into a String.

QueryField - Class in org.intermine.objectstore.query

Represents a QueryClass field that is neither a collection or reference to another business object.

QueryField(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField

Constructs a QueryField representing the specified field of a QueryClass

QueryField(Query, QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField

Constructs a QueryField representing the specified field of the specified QueryClass, as seen outside the specified subquery.

QueryField(Query, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryField

Constructs a QueryField representing the specified entry from the SELECT list of the specified subquery.

QueryField(QueryClassBag) - Constructor for class org.intermine.objectstore.query.QueryField

Constructs the id QueryField for the given QueryClassBag.

QueryField(FromElement, String, String, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryField

Constructs a QueryField object - intended for cloning operations.

QueryForeignKey - Class in org.intermine.objectstore.query

Represents the ID of a field of a QueryClass that is a business object

QueryForeignKey(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryForeignKey

Constructs a QueryForeignKey representing the specified field of a QueryClass

QueryForm - Class in org.intermine.web.struts

Action form that holds query XML.

QueryForm() - Constructor for class org.intermine.web.struts.QueryForm

queryForTypesInCollection(InterMineObject, String, ObjectStore) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper

Search for the classes in a collection for a given InterMineObject, for example find all of the sub-classes of Employee in the Department.employees collection of a given Department.

QueryFunction - Class in org.intermine.objectstore.query

A QueryFunction represents an aggregate

QueryFunction(QueryEvaluable, int) - Constructor for class org.intermine.objectstore.query.QueryFunction

QueryFunction(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryFunction

Constructor for functions that take two parameters.

QueryFunction() - Constructor for class org.intermine.objectstore.query.QueryFunction

Creates a COUNT aggregate function.

QueryGenUtil - Class in org.intermine.objectstore.querygen

Utility methods for paths.

QueryGenUtil.QueryAndClass - Class in org.intermine.objectstore.querygen

Class to allow returning of two arguments from a method.

QueryGenUtil.QueryAndClass(Query, Class<?>) - Constructor for class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass

Constructor.

QueryHelper - Class in org.intermine.objectstore.query

Static methods to assist with query generation from front end.

queryHistory - Variable in class org.intermine.api.profile.Profile

QueryListAppendService - Class in org.intermine.webservice.server.query

Append items to a list from the results of a query.

QueryListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryListAppendService

Constructor.

QueryListAppendServlet - Class in org.intermine.webservice.server.query

Runs the query-to-list service to run queries and save them as lists.

QueryListAppendServlet() - Constructor for class org.intermine.webservice.server.query.QueryListAppendServlet

QueryLogger - Class in org.intermine.sql.logging

Provides a logging facility for a Query

QueryMonitor - Interface in org.intermine.web.logic.query

Interface passed to SessionMethods runQuery method which is polled every so-often while the query runs in order to decide whether or not to cancel the query.

QueryMonitorTimeout - Class in org.intermine.web.logic.query

QueryMonitor that cancels a query after a given timeout period.

QueryMonitorTimeout(int) - Constructor for class org.intermine.web.logic.query.QueryMonitorTimeout

Construct a new instance of QueryMonitorTimeout.

queryName - Variable in class org.intermine.web.struts.SaveQueryForm

QueryNode - Interface in org.intermine.objectstore.query

An element that can appear in the SELECT, ORDER BY or GROUP BY clause of a query.

QueryObjectPathExpression - Class in org.intermine.objectstore.query

An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a object referenced by some other object in the results.

QueryObjectPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression

Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname.

QueryObjectPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression

Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname, constrained to be a particular subclass.

queryObjectPathExpressionToString(Query, List<Object>, QueryObjectPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts a QueryObjectPathExpression into a String.

QueryObjectReference - Class in org.intermine.objectstore.query

Represents a field of a QueryClass that is a business object

QueryObjectReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectReference

Constructs a QueryObjectReference representing the specified field of a QueryClass

QueryOptimiser - Class in org.intermine.sql.precompute

A static class providing the code to optimise a query, given a database (presumably with a table describing the available precomputed tables).

QueryOptimiser.AbstractTableComparator - Class in org.intermine.sql.precompute

Compares two AbstractTables using their equalsIgnoreAlias() method.

QueryOptimiser.AbstractTableComparator() - Constructor for class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator

Constructor.

QueryOptimiserContext - Class in org.intermine.sql.precompute

A class describing settings for the optimiser.

QueryOptimiserContext() - Constructor for class org.intermine.sql.precompute.QueryOptimiserContext

QueryOptimiserException - Exception in org.intermine.sql.precompute

An Exception that may be thrown by a QueryOptimiser method.

QueryOptimiserException() - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException

Constructs an QueryOptimiserException

QueryOptimiserException(String) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException

Constructs an QueryOptimiserException with the specified detail message.

QueryOptimiserException(Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException

Constructs an QueryOptimiserException with the specified nested throwable.

QueryOptimiserException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException

Constructs an QueryOptimiserException with the specified detail message and nested throwable.

QueryOrderable - Interface in org.intermine.objectstore.query

An element that can appear in the ORDER BY clause of a query.

QueryParseTimeoutException - Exception in org.intermine.sql.query

Exception thrown when parsing a query from SQL string to org.intermine.sql.Query object.

QueryParseTimeoutException() - Constructor for exception org.intermine.sql.query.QueryParseTimeoutException

QueryPathExpression - Interface in org.intermine.objectstore.query

An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results, usually in a separate database operation.

QueryPathExpressionWithSelect - Interface in org.intermine.objectstore.query

A Path Expression that has a Select list.

QueryReference - Class in org.intermine.objectstore.query

Represents a field of a QueryClass that is a non-primitive type.

QueryReference() - Constructor for class org.intermine.objectstore.query.QueryReference

queryReferenceToString(Query, QueryReference, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery

Converts a QueryReference into a String.

QueryRemovalService - Class in org.intermine.webservice.server.query

A service that removes a saved query from profile's collection of saved queries.

QueryRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRemovalService

QueryRequestParser - Class in org.intermine.webservice.server.query

Processes query request parameters.

QueryRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.QueryRequestParser

RequestProcessor constructor.

QueryResultInput - Class in org.intermine.webservice.server.query.result

QueryServiceInput is parameter object representing parameters for QueryResultService web service.

QueryResultInput() - Constructor for class org.intermine.webservice.server.query.result.QueryResultInput

QueryResultLinkGenerator - Class in org.intermine.webservice.server.query.result

Class that implements generating links for QueryResultService web service.

QueryResultLinkGenerator() - Constructor for class org.intermine.webservice.server.query.result.QueryResultLinkGenerator

QueryResultRequestParser - Class in org.intermine.webservice.server.query.result

Processes service request.

QueryResultRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.result.QueryResultRequestParser

RequestProcessor constructor.

QueryResultService - Class in org.intermine.webservice.server.query.result

Executes query and returns results.

QueryResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.QueryResultService

Constructor

QueryResultServlet - Class in org.intermine.webservice.server.query.result

Servlet that runs QueryResultService.

QueryResultServlet() - Constructor for class org.intermine.webservice.server.query.result.QueryResultServlet

QueryRetrieverService - Class in org.intermine.webservice.server.query

A service that retrieves a stored query by qid.

QueryRetrieverService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRetrieverService

QuerySelectable - Interface in org.intermine.objectstore.query

An element that can appear in the SELECT clause of a query.

QueryService - Class in org.intermine.webservice.client.services

The QueryService class provides a mechanism for sending data queries to an InterMine webservice, and retrieving and parsing the results.

QueryService(String, String) - Constructor for class org.intermine.webservice.client.services.QueryService

Constructor.

QueryService.NumericSummary - Class in org.intermine.webservice.client.services

Result format for Numeric Summary information.

QueryService.QueryRequest - Class in org.intermine.webservice.client.services

The request class for handling queries - in particular this class is responsible for handling the query parameters.

QueryService.QueryRequest(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.services.QueryService.QueryRequest

Constructor.

queryStore - Variable in class org.intermine.api.InterMineAPI

QueryStore - Interface in org.intermine.api.query

QueryStoreException - Exception in org.intermine.api.query

QueryStoreException(String, Exception) - Constructor for exception org.intermine.api.query.QueryStoreException

QueryStoreException(String) - Constructor for exception org.intermine.api.query.QueryStoreException

QueryStoreService - Class in org.intermine.webservice.server.query

A service that stores a query and associates it with an id.

QueryStoreService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryStoreService

queryString - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

queryString - Variable in class org.intermine.sql.precompute.BestQueryFallback

QueryToListService - Class in org.intermine.webservice.server.query

A service for transforming a query, represented as a PathQuery serialised to XML, to a list.

QueryToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryToListService

Constructor.

QueryToListServlet - Class in org.intermine.webservice.server.query

Runs the query-to-list service to run queries and save them as lists.

QueryToListServlet() - Constructor for class org.intermine.webservice.server.query.QueryToListServlet

queryToPathToQueryNode - Static variable in class org.intermine.api.query.QueryExecutor

A cache of pathToQueryNode maps that is shared between subclasses of QueryExecutor.

QueryTrack - Class in org.intermine.api.tracker.track

QueryTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.QueryTrack

QUERYTRACK - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding

label for XML

QueryTrackBinding - Class in org.intermine.api.tracker.xml

QueryTracker - Class in org.intermine.api.tracker

QueryTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.QueryTracker

Build a query tracker

QUERYTRACKS - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding

label for XML

QueryUpdateService - Class in org.intermine.webservice.server.query

Same in all respects as the upload service, but this class overwrites queries with the provided names.

QueryUpdateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUpdateService

QueryUploadService - Class in org.intermine.webservice.server.query

A service to enable queries to be uploaded programmatically.

QueryUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUploadService

Constructor.

QueryUploadServlet - Class in org.intermine.webservice.server.query

Runs the query Upload Service to handle user query uploads.

QueryUploadServlet() - Constructor for class org.intermine.webservice.server.query.QueryUploadServlet

QueryValue - Class in org.intermine.objectstore.query

Represents a constant in a Query

QueryValue(Object) - Constructor for class org.intermine.objectstore.query.QueryValue

Construct a QueryValue

queue - Variable in class org.intermine.util.ReferenceMap

queueMessage(MailAction) - Static method in class org.intermine.web.context.InterMineContext

Queue up a message to an emailer.

QuickSearch - Class in org.intermine.webservice.server.search

A service that runs key-word searches.

QuickSearch(InterMineAPI, ServletContext) - Constructor for class org.intermine.webservice.server.search.QuickSearch

QuickSearchJSONProcessor - Class in org.intermine.webservice.server.search

A class that renders quick search results as JSON.

QuickSearchJSONProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchJSONProcessor

QuickSearchResultProcessor - Interface in org.intermine.webservice.server.search

The type of objects that can handle keyword search results.

QuickSearchServlet - Class in org.intermine.webservice.server.search

QuickSearchServlet() - Constructor for class org.intermine.webservice.server.search.QuickSearchServlet

QuickSearchTextProcessor - Class in org.intermine.webservice.server.search

A result processor that outputs results as plain text.

QuickSearchTextProcessor(String) - Constructor for class org.intermine.webservice.server.search.QuickSearchTextProcessor

QuickSearchXMLProcessor - Class in org.intermine.webservice.server.search

A result processor that outputs results as XML.

QuickSearchXMLProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchXMLProcessor

R

rand - Static variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

random - Static variable in class org.intermine.web.task.LoadDefaultTemplatesTask

Range - Interface in org.intermine.api.query.range

range(int, int) - Method in class org.intermine.objectstore.query.Results

Returns a range of rows of results.

range(int, int) - Method in class org.intermine.objectstore.query.SingletonResults

Returns a range of rows of results.

RANGE_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager

Description of range type columns defined in the database.

rangeConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

RangeHelper - Interface in org.intermine.api.query

rangeHelpers - Static variable in class org.intermine.api.query.MainHelper.RangeConfig

rangeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

ranges - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

RateLimitException - Exception in org.intermine.webservice.server.exceptions

Exception representation for denying service based on rate limits.

RateLimitException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.RateLimitException

Constructor

RateLimitHistory - Class in org.intermine.webservice.server.core

A class for making sure that certain resources don't get hammered.

RateLimitHistory(int, int) - Constructor for class org.intermine.webservice.server.core.RateLimitHistory

Constructor

read() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream

read(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream

readBagQueryConfig(Model, InputStream) - Static method in class org.intermine.api.bag.BagQueryHelper

Read the bag query configuration from the given stream.

readConfig(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory

Read pid configurations from entrezIdResolver_config.properties in resources dir

readConfig() - Method in class org.intermine.bio.dataconversion.GFF3Converter

read in config file

readConfig() - Method in class org.intermine.bio.ontology.OboParser

Parses config file for valid prefixes, eg.

readKeys(Model, Properties) - Static method in class org.intermine.api.config.ClassKeyHelper

Read class keys from a properties into a map from classname to set of available keys.

readLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager

Returns an InputStream object with which to read a large binary value from the database.

readOneTestConfig(LineNumberReader) - Static method in class org.intermine.task.AcceptanceTestTask

Read and return one AcceptanceTest object from the given Reader.

ReadPreferencesService - Class in org.intermine.webservice.server.user

A service for reading the current state of a user's preferences.

ReadPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.ReadPreferencesService

readRelations(BufferedReader) - Method in class org.intermine.bio.ontology.OboParser

This method reads relations calculated by the GO2Link script in OBOEdit.

readTerms(BufferedReader) - Method in class org.intermine.bio.ontology.OboParser

Read DAG input line by line to generate hierarchy of DagTerms.

readWebProperties(Properties) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo

ReadWriteJSONService - Class in org.intermine.webservice.server.core

Convenience for services that need to combine JSON service behaviour with strict RW authorisation.

ReadWriteJSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.ReadWriteJSONService

Construct a read/write service.

realiseObjects(Collection<Item>, Model, boolean) - Static method in class org.intermine.xml.full.FullParser

Create business objects from a collection of Items.

realiseObjects(Collection<Item>, Model, boolean, boolean) - Static method in class org.intermine.xml.full.FullParser

Create business objects from a collection of Items.

ReallyFlatIterator - Class in org.intermine.api.results.flatouterjoins

An Iterator that flattens the contents of another Iterator.

ReallyFlatIterator(Iterator) - Constructor for class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

Constructs a ReallyFlatIterator from another Iterator.

rebuildClassIndexes() - Method in class org.intermine.web.autocompletion.LuceneIndex

rebuild all indexes from LuceneObjectClasses in the map

receiveEvent(ChangeEvent) - Method in class org.intermine.api.search.SearchRepository

receiveEvent(ChangeEvent) - Method in interface org.intermine.api.search.WebSearchWatcher

Receive notification of a change to a WebSearchable somewhere in the universe.

recentSequences - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

reconstruct(String) - Method in class org.intermine.sql.precompute.LimitOffsetQuery

Reconstruct a SQL string, given this alternative SQL query-part.

reconstructAbstractConstraint(AbstractConstraint, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Reconstructs an AbstractConstraint object, using reconstructAbstractValue.

reconstructAbstractConstraints(Set<AbstractConstraint>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Set<AbstractConstraint>, Set<AbstractConstraint>, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Populates the WHERE list of a new Query object, given the old Query's WHERE (or HAVING) list to use as a reference.

reconstructAbstractValue(AbstractValue, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Reconstructs an AbstractValue, to form the part of an SQL Query that has been replaced with a PrecomputedTable.

reconstructAbstractValues(Collection<AbstractValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Collection<AbstractValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Reconstructs a Collection of AbstractValue objects, calling reconstructAbstractValue on each one before adding it to another Collection.

reconstructSelectValues(List<SelectValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Populates the SELECT list of a new Query object, given an old Query's SELECT list to use as a reference, a valueMap (to pass to reconstructAbstractValue), and a Table to represent the PrecomputedTable.

recordError(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Record an error.

recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineAction

Add the given ActionMessage as an error for this Action and log the error

recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineDispatchAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineDispatchAction

Add the given ActionMessage as an error for this Action and log the error

recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction

Add the given ActionMessage as an error for this Action

recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction

Add the given ActionMessage as an error for this Action and log the error

recordMessage(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Record a message that will be stored in the session until it is displayed to the user.

recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction

Add the given ActionMessage as a message for this Action

recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction

Add the given ActionMessage as a message for this Action

recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction

Add the given ActionMessage as a message for this Action

recordRequest(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory

Record that a request was made.

recursiveOptimise(Set<PrecomputedTable>, Query, BestQuery, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.

recursiveOptimiseCheckSubquery(Set<PrecomputedTable>, Query, BestQuery) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.

ref - Variable in class org.intermine.objectstore.query.ContainsConstraint

REFERENCE - Static variable in class org.intermine.api.tag.TagTypes

Reference.

Reference - Class in org.intermine.xml.full

Representation of an Reference in an object

Reference() - Constructor for class org.intermine.xml.full.Reference

Constructor

Reference(String, String) - Constructor for class org.intermine.xml.full.Reference

Construnctor

REFERENCE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

The lists to subtract from

ReferenceList - Class in org.intermine.xml.full

Representation of a field in an object.

ReferenceList() - Constructor for class org.intermine.xml.full.ReferenceList

Constructor

ReferenceList(String) - Constructor for class org.intermine.xml.full.ReferenceList

Constructor

ReferenceList(String, List<String>) - Constructor for class org.intermine.xml.full.ReferenceList

Constructor

ReferenceMap<K,V> - Class in org.intermine.util

This is a Map implementation designed specifically for people intending to create a cache.

ReferenceMap() - Constructor for class org.intermine.util.ReferenceMap

ReferenceMap.ReferenceWithKey<K> - Interface in org.intermine.util

Interface for entries in the map.

refIds - Variable in class org.intermine.xml.full.ReferenceList

refsAndCollections - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

register(String, String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory

Register exporter.

registerObject(Object) - Static method in class org.intermine.util.ShutdownHook

Registers an object with the shutdown hook.

registerOffset(Query, int, DatabaseSchema, Database, Object, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Registers an offset for a given query.

registerRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

This method registers a Thread with a request ID.

registerStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

This method registers a Statement with the current Thread's request ID, or throws an exception if that request is black-listed, or does nothing if no request ID is present for this Thread.

Registrar - Class in org.intermine.web.struts

A class to handle registration of mines with a registry service.

Registrar(Properties) - Constructor for class org.intermine.web.struts.Registrar

Constructor

rejectInvitation(SharingInvite) - Static method in class org.intermine.api.bag.SharedBagManager

Reject this invitation.

RELATED_DATA_CONSTRAINT_1 - Static variable in class org.intermine.api.config.Constants

Constraint for related data template

RELATED_DATA_CONSTRAINT_2 - Static variable in class org.intermine.api.config.Constants

Constraint for related data template

RELATED_DATA_TEMPLATE - Static variable in class org.intermine.api.config.Constants

queries for data related to current object

relations - Variable in class org.intermine.bio.ontology.OboParser

All relations

RelativeComplement - Class in org.intermine.api.bag.operations

RelativeComplement(Model, Profile, Collection<InterMineBag>, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.RelativeComplement

releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Allows one to put a connection back.

releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Allows one to put a connection back.

ReleaseEtagFilter - Class in org.intermine.web.filters

Return responses tagged with the release version.

ReleaseEtagFilter() - Constructor for class org.intermine.web.filters.ReleaseEtagFilter

releaseGoFaster() - Method in class org.intermine.api.results.ExportResultsIterator

Switches off the goFaster mode in the objectstore for this query.

releaseGoFaster() - Method in class org.intermine.api.results.WebResults

Calls ObjectStore.releaseGoFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.

releaseGoFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Releases the resources used by goFaster().

releaseResources(ResultSet, Statement) - Method in class org.intermine.api.tracker.AbstractTracker

Close the result set and statement objects specified in input

releaseResources() - Method in class org.intermine.api.tracker.xml.TrackHandler

remapAliases(Map<AbstractTable, AbstractTable>, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Alters all the aliases of the tables being mapped to, to equal the alias of the table mapping to them.

remapAliasesToAvoidPrecomputePrefix(Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser

Remaps the aliases of any table that starts with the ALIAS_PREFIX, to avoid clashes with future precomputed tables.

RemoteMine - Class in org.intermine.api.mines

An object that represents an InterMine application hosted somewhere else.

RemoteMine(String, MineRequester, int) - Constructor for class org.intermine.api.mines.RemoteMine

Create a representation of a remotely accessible mine.

remove(Object) - Method in class org.intermine.api.profile.UserPreferences

remove() - Method in class org.intermine.api.results.ExportResultsIterator

This method is not supported.

remove() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator

This operation is not supported.

remove(Object) - Method in class org.intermine.util.AlwaysMap

remove() - Method in class org.intermine.util.CombinedIterator

This operation is not supported.

remove(Object) - Method in class org.intermine.util.IdentityMap

remove() - Method in class org.intermine.util.ObjectPipe

remove(Object) - Method in class org.intermine.util.PseudoSet

remove(Object) - Method in class org.intermine.util.ReferenceMap

remove() - Method in class org.intermine.util.SynchronisedIterator

remove(Object) - Method in class org.intermine.webservice.client.lists.ItemList

remove(Object) - Method in class org.intermine.webservice.client.results.ResultRowList

remove(int) - Method in class org.intermine.webservice.client.results.ResultRowList

remove() - Method in class org.intermine.webservice.server.core.TableRowIterator

remove() - Method in class org.intermine.webservice.server.output.FilteringResultIterator

remove() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator

remove() - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Remove is not supported.

remove() - Method in class org.intermine.webservice.server.output.JSONRowIterator

remove() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator

removeAll(Collection<?>) - Method in class org.intermine.util.PseudoSet

removeAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList

removeAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList

removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Removes a collection of elements from an ObjectStoreBag, delegate to internal ObjectStoreWriter.

removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Removes a collection of elements from an ObjectStoreBag.

removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Removes a collection of elements from an ObjectStoreBag.

removeAllFromBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Removes elements from the given bag.

removeAllInvitesBy(Integer) - Method in class org.intermine.api.bag.SharedBagManager

Removes all invitations to share resources that were issued by the user with the given id.

removeAllIrrelevant() - Method in class org.intermine.pathquery.PathQuery

Removes everything from this query that is irrelevant, and therefore making the query invalid.

removeAllSharesInvolving(Integer) - Method in class org.intermine.api.bag.SharedBagManager

Removes all shares from or to the user with the given id.

removeAllTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil

Removes every single table from the database given.

removeAllUnder(String) - Method in class org.intermine.pathquery.PathQuery

Removes everything under a given path from the query, such that if the query was valid before, it will be valid after this method.

removeAllVariablesExcept(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression

Remove any variables that aren't in the given set.

removeAttribute(String) - Method in class org.intermine.xml.full.Item

Remove a attribute of the specified name if it exists.

removeCollection(String) - Method in class org.intermine.xml.full.Item

Remove a collection of the specified name if it exists.

removeConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet

Remove specified constraint

removeConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery

Removes a constraint from this query.

removeConstraint(PathConstraint) - Method in class org.intermine.template.TemplateQuery

Removes a constraint from this query.

removeConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Remove a constraint identified by its code from the query.

removeDirectAttributesFromView(TemplateQuery) - Static method in class org.intermine.api.template.TemplateHelper

Removed from the view all the direct attributes that aren't editable constraints

removeEldestEntry(Map.Entry) - Method in class org.intermine.api.util.LimitedMap

removeFeature() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Remove the feature item that was set with setFeature() and associated synonyms

removeFieldDescriptor(Set<? extends FieldDescriptor>, String) - Static method in class org.intermine.modelproduction.ModelMerger

Remove a FieldDescriptor from a Set of FieldDescriptors by name.

removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Removes an element from an ObjectStoreBag, delegate to internal ObjectStoreWriter.

removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Removes an element from an ObjectStoreBag.

removeFromBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Removes an element from an ObjectStoreBag.

removeFromConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper

Remove a constraint code from a logic expression, e.g.

removeFromView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange

Remove a Node from the results view

removeIdFromBag(Integer) - Method in class org.intermine.api.profile.InterMineBag

Remove the given id from the bag, this updates the bag contents in the database

removeIdsFromBag(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag

Remove the given ids from the bag, this updates the bag contents in the database

removeJob(String) - Method in class org.intermine.api.idresolution.IDResolver

removeNode(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Remove everything in a query under a given path.

removeObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag

removeObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable

Remove this observer from the list of interested parties.

removeObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate

removeOrderBy(String) - Method in class org.intermine.pathquery.PathQuery

Removes an element from the order by list of this query.

removePermanentToken(PermanentToken) - Method in class org.intermine.api.profile.ProfileManager

removeQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods

Removes the current query from the session.

removeRedundancy(Map<String, ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger

When changes are made to the inheritance hierarchy (especially the addition of superinterfaces), fields may be defined on superinterfaces making previous definitions further down the inheritance hierarchy redundant.

removeReference(String) - Method in class org.intermine.xml.full.Item

Remove a reference of the specified name if it exists.

removeSelectedFromBag(InterMineBag, HttpSession) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

remove the selected elements from the bag.

removeSequence(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil

Remove the sequence from the database given.

removeSubclass(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Remove a subclass constraint from the query.

removeSubclassAndFixUp(String) - Method in class org.intermine.pathquery.PathQuery

Removes a subclass from the query, and removes any parts of the query that relied on it.

removeTags(String...) - Method in class org.intermine.webservice.client.lists.ItemList

Remove some tags from this list.

removeTags(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService

Get the tags for a list after removing some from its tag set.

removeTempBagTable(Connection, ObjectStoreInterMineImpl.BagTableToRemove) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Removes a temporary bag table, given a BagTableToRemove object.

removeToken(DeletionToken) - Method in class org.intermine.webservice.server.user.DeletionTokens

Remove this token.

removeTokensForProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager

Remove auth tokens for a specified users.

removeVariable(String) - Method in class org.intermine.pathquery.LogicExpression

Remove a variable from the expression.

removeView(String) - Method in class org.intermine.pathquery.PathQuery

Removes a single element from the view list.

removeView(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil

Remove the view from the database given.

rename(String) - Method in class org.intermine.api.profile.InvalidBag

Returns a new Invalid Bag identical to this one, but with the given name.

RENAME - Static variable in class org.intermine.api.profile.ModelUpdate

label in modelUpdate.properties file to identify renamed classes or fields

rename(String, String, String) - Method in class org.intermine.dwr.AjaxServices

Rename a element such as history, name, bag

rename(String) - Method in class org.intermine.webservice.client.lists.ItemList

Rename this list on the server.

rename(ItemList, String) - Method in class org.intermine.webservice.client.services.ListService

Rename a list on the server, returning a list representing the new state.

renameBag(String, String) - Method in class org.intermine.api.profile.Profile

Rename an existing bag, throw exceptions when bag doesn't exist of if new name already exists.

renameHistory(String, String) - Method in class org.intermine.api.profile.Profile

Rename an item in the history.

render(Object) - Static method in class org.intermine.objectstore.intermine.NotXmlRenderer

Render the given object as NotXml.

render(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer

Render a collection of objects as XML in InterMine Full format.

render(FastPathObject, Model) - Static method in class org.intermine.xml.full.FullRenderer

Render an Object as Xml in Full Data format.

render(Collection<Item>) - Static method in class org.intermine.xml.full.FullRenderer

Render a collection of items in InterMine Full XML format.

render(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer

Render the given Item as XML using an XMLStreamWriter

render(Item) - Static method in class org.intermine.xml.full.FullRenderer

Render the given Item as XML

RendererComparator - Class in org.intermine.xml.full

An implementation of Comparator to order pairs of Class objects.

RendererComparator() - Constructor for class org.intermine.xml.full.RendererComparator

renderImpl(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer

Render the given Item as XML using an XMLStreamWriter

reorder(String, String) - Method in class org.intermine.dwr.AjaxServices

AJAX request - reorder view.

reorderConstraints(String, String) - Method in class org.intermine.dwr.AjaxServices

AJAX request - reorder the constraints.

REPLACE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

Whether to overwrite existing lists of the same name

replaceClob(Clob, String) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Replaces the contents of the given Clob with the given String.

replaceClob(Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Replaces the contents of the given Clob with the given String.

replaceClob(Clob, String) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Replaces the contents of the given Clob with the given String.

replaceClobWithConnection(Connection, Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Replaces the contents of the given Clob with the given String.

replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.pathquery.PathQuery

Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.

replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.template.TemplateQuery

Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.

replaceSpecialChars(String) - Static method in class org.intermine.api.util.NameUtil

Takes a string and replaces special characters with the text value, e.g. it would change "a&b" to "a_AMPERSAND_b".

replaceStrain(Integer) - Static method in class org.intermine.bio.util.BioUtil

Looks in the organism repo for the taxon ID provided.

REPORT_OBJECT_CACHE - Static variable in class org.intermine.web.logic.Constants

The session attribute that holds the ReportObjectCache object for the session.

REPORT_TEMPLATE - Static variable in class org.intermine.api.config.Constants

checks for object in other mine

ReportAspectController - Class in org.intermine.web.struts

Controller for the reportAspect tile.

ReportAspectController() - Constructor for class org.intermine.web.struts.ReportAspectController

ReportController - Class in org.intermine.web.struts

New objectDetails.

ReportController() - Constructor for class org.intermine.web.struts.ReportController

ReportDisplayer - Class in org.intermine.web.displayer

Parent class for report displayers that appear on report pages.

ReportDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.web.displayer.ReportDisplayer

Construct with config information read from webconfig-model.xml and the API.

ReportDisplayerConfig - Class in org.intermine.web.logic.config

Bean to hold configuration for report displayers.

ReportDisplayerConfig() - Constructor for class org.intermine.web.logic.config.ReportDisplayerConfig

ReportDisplayerController - Class in org.intermine.web.struts

Execute a ReportDisplayer placed on the context.

ReportDisplayerController() - Constructor for class org.intermine.web.struts.ReportDisplayerController

reportDone(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager

Allows a system to report that it has finished servicing a particular request.

ReportInList - Class in org.intermine.web.logic.results

Wrapper, mainly to provide size

ReportInList(Collection<InterMineBag>) - Constructor for class org.intermine.web.logic.results.ReportInList

Setup

ReportInListController - Class in org.intermine.web.struts

ReportInListController() - Constructor for class org.intermine.web.struts.ReportInListController

ReportObject - Class in org.intermine.web.logic.results

Object to be displayed on report.do

ReportObject(InterMineObject, WebConfig, InterMineAPI, Properties) - Constructor for class org.intermine.web.logic.results.ReportObject

Setup internal ReportObject

ReportObject.TitleValue - Class in org.intermine.web.logic.results

Holder for formatted and unformatted versions of a title part.

ReportObjectFactory - Class in org.intermine.web.logic.results

A factory for ReportObjects.

ReportObjectFactory(InterMineAPI, WebConfig, Properties) - Constructor for class org.intermine.web.logic.results.ReportObjectFactory

Create a new ReportObjectCache for the given session.

ReportObjectField - Class in org.intermine.web.logic.results

Object field, used in header the summary of ReportObject

ReportObjectField(String, String, Object, String, boolean, boolean) - Constructor for class org.intermine.web.logic.results.ReportObjectField

Constructor

ReportObjectField(String, String, Object, String, boolean, boolean, String) - Constructor for class org.intermine.web.logic.results.ReportObjectField

Constructor

ReportTemplateController - Class in org.intermine.web.struts

Controller for an inline table created by running a template on a report page.

ReportTemplateController() - Constructor for class org.intermine.web.struts.ReportTemplateController

Request - Interface in org.intermine.webservice.client.core

Client request interface.

request - Variable in class org.intermine.webservice.server.lists.ListInput

request - Variable in class org.intermine.webservice.server.query.QueryRequestParser

request - Variable in class org.intermine.webservice.server.WebService

The servlet request.

Request.RequestType - Enum in org.intermine.webservice.client.core

RequestImpl - Class in org.intermine.webservice.client.core

Implementation of Request interface.

RequestImpl(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.core.RequestImpl

Constructor.

requestIsOfSuitableType() - Method in class org.intermine.webservice.server.lists.ListUploadService

Determine if we should service this request.

RequestPasswordAction - Class in org.intermine.web.struts

Action to handle button presses RequestPasswordForm

RequestPasswordAction() - Constructor for class org.intermine.web.struts.RequestPasswordAction

RequestPasswordForm - Class in org.intermine.web.struts

Form used to request a password

RequestPasswordForm() - Constructor for class org.intermine.web.struts.RequestPasswordForm

RequestSubClassFilter - Class in org.intermine.webservice.server.filter

Filter to wrap all web service requests in a custom delegating wrapper that prevents sessions being created.

RequestSubClassFilter() - Constructor for class org.intermine.webservice.server.filter.RequestSubClassFilter

requestURL(String, ContentType) - Method in class org.intermine.api.mines.HttpRequester

requestURL(String, ContentType) - Method in interface org.intermine.api.mines.MineRequester

Request information as encoded in a string.

RequestUtil - Class in org.intermine.web.logic

Util methods for HttpServletRequest.

RESERVED_KEYS - Static variable in class org.intermine.webservice.server.output.JSONFormatter

keys which you aren't allowed to set.

reset() - Static method in class org.intermine.api.query.MainHelper.RangeConfig

reset

reset() - Method in class org.intermine.bio.dataconversion.UniprotEntry

this temporary variable is set whilst we are processing items that span multiple XML tags.

reset() - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory

Remove instance, used for testing only

reset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Resets the IntegrationWriter, clearing the id map and the hints

reset() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Resets the IntegrationWriter, clearing the id map and the hints

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BuildBagForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangeTableSizeForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm

Reset form bean.

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EditPropertiesForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.FindInListForm

Reset form bean.

reset() - Method in class org.intermine.web.struts.ImportQueriesForm

Reset the form.

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportTagsForm

reset() - Method in class org.intermine.web.struts.ImportTagsForm

Reset the form.

reset() - Method in class org.intermine.web.struts.ImportXMLForm

Reset the form.

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportXMLForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.InvitationForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifySuperUserForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.RequestPasswordForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveBagForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TableExportForm

Reset the form to the initial state

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateForm

reset() - Method in class org.intermine.web.struts.TemplateForm

Reset the form

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm

Reset the form bean taking initial state from current TemplateBuildState session attribute.

reset() - Method in class org.intermine.web.struts.TemplatesImportForm

Reset the form.

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.WidgetForm

ResolutionJob - Class in org.intermine.api.idresolution

ResolutionJob(UUID, BagQueryRunner, JobInput) - Constructor for class org.intermine.api.idresolution.ResolutionJob

resolveCollectionPath(Path, Object) - Static method in class org.intermine.api.util.PathUtil

Return the object at the end of a given path, starting from the given object.

resolveId(String, String) - Method in class org.intermine.bio.dataconversion.DoNothingIdResolver

resolveId(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

For the given id return a set of matching primary identifiers in the given taxonId.

resolveId(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver

For the given id return a set of matching primary identifiers in the given taxonId.

resolveIds(String, String, List<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

For the given set of ids return a map of matching primary identifiers in the given taxonId.

resolveIds(String, List<String>) - Method in class org.intermine.bio.dataconversion.IdResolver

For the given id set return a map of matching primary identifiers in the given taxonId.

resolveInvitation(SharingInvite, Profile, boolean) - Method in class org.intermine.api.bag.SharedBagManager

Either reject or accept an invitation to share a list.

resolvePath(Path, Object) - Static method in class org.intermine.api.util.PathUtil

Return the object at the end of a given path, starting from the given object.

resolver - Static variable in class org.intermine.bio.dataconversion.IdResolverFactory

ResourceFinder - Class in org.intermine.web.struts

A class for finding resources in the WEB-INF directory at run-time based on patterns.

ResourceFinder(ServletContext) - Constructor for class org.intermine.web.struts.ResourceFinder

Constructor.

ResourceNotFoundException - Exception in org.intermine.webservice.client.exceptions

The ResourceNotFoundException is thrown by a service provider when an attempt is made to perform an operation upon a resource that cannot be found.

ResourceNotFoundException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException

ResourceNotFoundException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException

ResourceNotFoundException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException

ResourceNotFoundException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException

ResourceNotFoundException - Exception in org.intermine.webservice.server.exceptions

The ResourceNotFoundException is thrown by a service provider when an attempt is made to perform an operation upon a resource that cannot be found.

ResourceNotFoundException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException

ResourceNotFoundException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException

ResourceNotFoundException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException

ResourceOpener - Interface in org.intermine.web.logic

The type of objects that can open resources by names.

resourceUrl - Variable in class org.intermine.webservice.client.core.Service

respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet

Respond to a request.

respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet

respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet

respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.PermaTokensServlet

response - Variable in class org.intermine.webservice.server.WebService

The servlet response.

ResponseType - Enum in org.intermine.web.struts.oauth2

ResponseUtil - Class in org.intermine.web.logic.export

Response util that sets content type and header for various formats and has util methods for setting headers controlling cache.

RestfulServlet - Class in org.intermine.webservice.server.core

RestfulServlet() - Constructor for class org.intermine.webservice.server.core.RestfulServlet

restoreFromFile(Set<String>) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory

Populate the ID resolver from a cached file

restoreFromFile(File) - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Read IdResolver contents from a file, allows for caching during build.

restoreFromFile() - Method in class org.intermine.bio.dataconversion.IdResolverFactory

Read IdResolver contents from a file, allows for caching during build.

ResultCell - Interface in org.intermine.api.results

An interface for result cells

ResultElement - Class in org.intermine.api.results

Cell of results table containing information for the parent Object

ResultElement(FastPathObject, Path, boolean) - Constructor for class org.intermine.api.results.ResultElement

Constructs a new ResultCell object

ResultElement(Object) - Constructor for class org.intermine.api.results.ResultElement

Create a ResultElement that displays a single raw value.

ResultElementConverter - Class in org.intermine.web.logic.export

ResultElementConverter() - Constructor for class org.intermine.web.logic.export.ResultElementConverter

ResultException - Exception in org.intermine.webservice.client.exceptions

ResultException is the exception thrown when a request fails.

ResultException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException

ResultException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException

ResultException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException

ResultException(String, String) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException

Construct an informative exception.

ResultProcessor - Class in org.intermine.webservice.server.core

Processor of Results object for easy accessing and parsing of results to list of strings.

ResultProcessor() - Constructor for class org.intermine.webservice.server.core.ResultProcessor

Constructor.

ResultRowList - Class in org.intermine.webservice.client.results

A representation of a result row that allows parsed objects to be retrieved by index, where the order of elements is the same as that of the view list of the originating PathQuery.

ResultRowList(JSONArray) - Constructor for class org.intermine.webservice.client.results.ResultRowList

Construct a new result row object backed by the given JSONArray.

ResultRowList(String) - Constructor for class org.intermine.webservice.client.results.ResultRowList

Construct a new result row object backed by the JSONArray which can be parsed from the given String.

ResultRowMap - Class in org.intermine.webservice.client.results

A class that represents a row of a result set as a map from column names to values.

ResultRowMap(JSONArray, List<String>) - Constructor for class org.intermine.webservice.client.results.ResultRowMap

Construct a result-row with a JSONArray as its backing data store.

ResultRowMap(String, List<String>) - Constructor for class org.intermine.webservice.client.results.ResultRowMap

Construct a result-row with a String as its backing data store.

ResultRowParser - Interface in org.intermine.webservice.server.core

Interface of parser that parses row of results to list of strings.

results - Variable in class org.intermine.api.results.ExportResultsIterator

results - Variable in class org.intermine.objectstore.query.ClobAccess

Results - Class in org.intermine.objectstore.query

Results representation as a List of ResultRows.

Results() - Constructor for class org.intermine.objectstore.query.Results

No argument constructor for testing purposes

Results(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.Results

Constructor for a Results object.

Results(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.Results

Constructor for a Results object, given a ResultsBatches object.

results - Variable in class org.intermine.web.logic.results.InlineResultsTable

results(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction

Load a template from template name passed as parameter.

RESULTS_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store the size of table with results.

ResultsAction - Class in org.intermine.web.struts

ResultsAction is called before results table is rendered.

ResultsAction() - Constructor for class org.intermine.web.struts.ResultsAction

resultsAsList - Variable in class org.intermine.web.logic.results.InlineResultsTable

resultsBatches - Variable in class org.intermine.objectstore.query.Results

ResultsBatches - Class in org.intermine.objectstore.query

Class holding the data batches for the Results object.

ResultsBatches(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.ResultsBatches

Construct a new ResultsBatches object.

resultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

ResultsConverter - Class in org.intermine.objectstore.intermine

Provides a method to convert from SQL ResultSet data to InterMine object-based data.

ResultSet - Class in org.intermine.webservice.client.results

Common behaviour and interface for result sets.

ResultSet(HttpConnection) - Constructor for class org.intermine.webservice.client.results.ResultSet

Constructor.

ResultSet(String) - Constructor for class org.intermine.webservice.client.results.ResultSet

Constructor with a String.

ResultSet(BufferedReader) - Constructor for class org.intermine.webservice.client.results.ResultSet

Constructor with a reader.

ResultsFlatOuterJoinsImpl - Class in org.intermine.api.results.flatouterjoins

Provides an implementation of List that encapsulates another List (like a Results object), and translates row into flat MultiRow format in a way suitable for displaying in the webapp.

ResultsFlatOuterJoinsImpl(List<ResultsRow>, Query) - Constructor for class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

Constructor for this object.

ResultsInfo - Class in org.intermine.objectstore.query

Represents a result from the estimate() method of an ObjectStore.

ResultsInfo() - Constructor for class org.intermine.objectstore.query.ResultsInfo

No-arg constructor to allow serialization

ResultsInfo(long, long, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo

Constructs an instance of ResultsInfo with all new parameters, without min and max.

ResultsInfo(long, long, int, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo

Constructs an instance of ResultsInfo with all new parameters.

ResultsInfo(ResultsInfo, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo

Constructs an instance of ResultsInfo from another ResultsInfo and a new min and max.

ResultsRow<E> - Class in org.intermine.objectstore.query

ResultsRow() - Constructor for class org.intermine.objectstore.query.ResultsRow

ResultsRow(Collection<? extends E>) - Constructor for class org.intermine.objectstore.query.ResultsRow

ResultsWithFacets - Class in org.intermine.api.lucene

A class that wraps both a collection of hits and a collection of facets.

ResultsWithFacets(Collection<KeywordSearchHit>, Collection<KeywordSearchFacet>, int) - Constructor for class org.intermine.api.lucene.ResultsWithFacets

retainAll(Collection<?>) - Method in class org.intermine.util.PseudoSet

retainAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList

retrieve(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager

Retrieve the value for a given key from the metadata table of the database

retrieveBag(String) - Method in class org.intermine.webservice.server.widget.WidgetService

Get the bag in question.

retrieveBLOBInputStream(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager

Retrieve the BLOB value for a given key from the metadata table of the database

retrieveExplainString(Statement) - Method in class org.intermine.sql.query.PostgresExplainResult

Retrieve EXPLAIN String from post-7.3 databases

RetrieveMetadataTask - Class in org.intermine.task

Retrieve the model metadata from a database

RetrieveMetadataTask() - Constructor for class org.intermine.task.RetrieveMetadataTask

retrieveToken(UUID) - Method in class org.intermine.webservice.server.user.DeletionTokens

Retrieve a token by its identifier.

returnNewTableRow() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable

Create a table row object

returnNewTableRow() - Method in class org.intermine.web.logic.results.InlineResultsTable

Create a table row object, overriden on BagUploadConfirm where we go custom

returnToString - Variable in class org.intermine.web.struts.LoginForm

RgdIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion

ID resolver for RGD genes.

RgdIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory

Construct with SO term of the feature type.

RgdIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory

Construct with SO term of the feature type.

right - Variable in class org.intermine.objectstore.query.OverlapConstraint

right - Variable in class org.intermine.sql.query.Constraint

right - Variable in class org.intermine.sql.query.InListConstraint

right - Variable in class org.intermine.sql.query.SubQueryConstraint

RIGHT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the right is always false.

RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint

Describes two constraints, where the right is always true.

ROUND - Static variable in class org.intermine.objectstore.query.QueryFunction

Round to a given number of decimal places.

Row - Class in org.intermine.sql.writebatch

Stores two ints.

Row(int, int) - Constructor for class org.intermine.sql.writebatch.Row

Constructor.

RowFormatter - Interface in org.intermine.web.logic.export

Interface denoting that object is able format list of objects to string.

RowFormatterImpl - Class in org.intermine.web.logic.export

Implements RowFormatter interface.

RowFormatterImpl(String, boolean) - Constructor for class org.intermine.web.logic.export.RowFormatterImpl

Constructor.

rowObjects - Variable in class org.intermine.web.logic.results.InlineResultsTable

RowResultSet - Class in org.intermine.webservice.client.results

A class for managing results received as a jsonrows result-set.

RowResultSet(HttpConnection, List<String>, int) - Constructor for class org.intermine.webservice.client.results.RowResultSet

Construct a new result-set with an HttpConnection and a list of output columns.

RowResultSet(BufferedReader, List<String>, int) - Constructor for class org.intermine.webservice.client.results.RowResultSet

Constructor with a reader.

RowResultSet(String, List<String>) - Constructor for class org.intermine.webservice.client.results.RowResultSet

Construct a new result-set from a string and a list of output columns.

rows - Variable in class org.intermine.objectstore.query.ResultsInfo

rows - Variable in class org.intermine.sql.query.ExplainResult

rslv - Variable in class org.intermine.bio.dataconversion.BioGridConverter

rslv - Variable in class org.intermine.bio.dataconversion.GoConverter

rslv - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter

rslv - Variable in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor

rslv - Variable in class org.intermine.bio.dataconversion.PsiConverter

rslv - Variable in class org.intermine.bio.dataconversion.PubMedGeneConverter

rslv - Variable in class org.intermine.bio.dataconversion.UniprotConverter

run() - Method in interface org.intermine.api.idresolution.Job

run job

run() - Method in class org.intermine.api.idresolution.ResolutionJob

run() - Method in class org.intermine.api.idresolution.UpgradeJob

run() - Method in class org.intermine.api.lucene.InterMineObjectFetcher

fetch objects from database, create documents and add them to the queue

run() - Method in class org.intermine.api.tracker.TrackerLogger

run(PreparedStatement) - Method in class org.intermine.objectstore.intermine.SQLOperation

The code that the operation represents.

run() - Method in class org.intermine.util.ShutdownHook

run() - Method in class org.intermine.web.context.MailDaemon

run() - Method in class org.intermine.web.logic.profile.UpgradeBagList

run(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction

Excecute a query.

run() - Method in class org.intermine.web.struts.Registrar

Send a post request to the registry service, if one has been set up.

run() - Method in class org.intermine.webservice.server.idresolution.JobJanitor

runAllTests(Database, LineNumberReader) - Method in class org.intermine.task.AcceptanceTestTask

Run all the tests and return a List of AcceptanceTestResult objects.

runBagUpgrade(UpgradeBagList, InterMineAPI, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler

Kick off a bag upgrade for current user.

runBrowseSearch(String, int, Map<String, String>, List<Integer>, int) - Static method in class org.intermine.api.lucene.KeywordSearch

perform a keyword search using bobo-browse for faceting and pagination

runBrowseSearch(String, int, Map<String, String>, List<Integer>, boolean, int) - Static method in class org.intermine.api.lucene.KeywordSearch

perform a keyword search using bobo-browse for faceting and pagination

runBrowseWithFacets(InterMineAPI, String, int, Map<String, String>, List<Integer>) - Static method in class org.intermine.api.lucene.KeywordSearch

Run a browse search and get back both search results and facet information.

RunIqlQueryTask - Class in org.intermine.task

Ant task to read an IQL query from a -Dquery="QUERY" parameter and execute it in the database.

RunIqlQueryTask() - Constructor for class org.intermine.task.RunIqlQueryTask

runLuceneSearch(String) - Static method in class org.intermine.api.lucene.KeywordSearch

Deprecated.

Use runBrowseSearch instead.

runLuceneSearch(String, SearchTarget, SearchRepository) - Static method in class org.intermine.api.search.SearchResults

Search a Lucene index and return a search result.

RUNNING_QUERIES - Static variable in class org.intermine.web.logic.Constants

Session attribute.

runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.QueryResultService

Runs path query and returns to output obtained results.

runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.TableRowService

runQuery(HttpSession, MessageResources, String, SessionMethods.Action, SessionMethods.CompletionCallBack) - Static method in class org.intermine.web.logic.session.SessionMethods

Executes an action and call a callback when it completes successfully.

RunQueryAction - Class in org.intermine.web.struts

Run a query as passed in directly as XML.

RunQueryAction() - Constructor for class org.intermine.web.struts.RunQueryAction

runTemplate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

Show in table for inline template queries.

S

SAFENESS_ANTISAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

Safeness value indicating a situation safe for ContainsConstraint DOES NOT CONTAIN

SAFENESS_SAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

Safeness value indicating a situation safe for ContainsConstraint CONTAINS

SAFENESS_UNSAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

Safeness value indicating a situation unsafe for ContainsConstraint

save() - Method in class org.intermine.api.bag.SharingInvite

save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction

Save a query from the history.

saveBag(InterMineBag) - Method in class org.intermine.api.profile.Profile

Stores a new bag in the profile.

saveBag(String, InterMineBag) - Method in class org.intermine.api.profile.Profile

Stores a new bag in the profile.

saveBag(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction

Save the selected objects to a bag on the session

SaveBagAction - Class in org.intermine.web.struts

Saves selected items in a new bag or combines with existing bag.

SaveBagAction() - Constructor for class org.intermine.web.struts.SaveBagAction

saveBagDescription(String, String) - Method in class org.intermine.dwr.AjaxServices

For a given bag, set its description

SaveBagForm - Class in org.intermine.web.struts

Form bean for the results table and bag creation form.

SaveBagForm() - Constructor for class org.intermine.web.struts.SaveBagForm

Constructor

saveClassKeys(String, File) - Static method in class org.intermine.modelproduction.MetadataManager

Save the class keys, in serialized form, to the specified directory

SAVED_BAG_STATUS - Static variable in class org.intermine.web.logic.Constants

key for the map saved in the session containing the status of saved bags

savedBagId - Variable in class org.intermine.api.profile.StorableBag

savedBags - Variable in class org.intermine.api.profile.Profile

savedCounts - Variable in class org.intermine.dataloader.HintingFetcher

savedInvalidBags - Variable in class org.intermine.api.profile.Profile

savedQueries - Variable in class org.intermine.api.profile.Profile

SavedQuery - Class in org.intermine.api.profile

Container for a saved query.

SavedQuery(String, Date, PathQuery) - Constructor for class org.intermine.api.profile.SavedQuery

Construct a new instance of SavedQuery.

SavedQueryBinding - Class in org.intermine.api.xml

Convert SavedQuerys to and from XML

SavedQueryHandler - Class in org.intermine.api.xml

Extension of PathQueryHandler to handle parsing SavedQuerys

SavedQueryHandler(Map<String, SavedQuery>, Map, int) - Constructor for class org.intermine.api.xml.SavedQueryHandler

Constructor

SavedQueryRetrievalService - Class in org.intermine.webservice.server.query

SavedQueryRetrievalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.SavedQueryRetrievalService

savedTemplateQuery - Variable in class org.intermine.api.template.ApiTemplate

SavedTemplateQuery object in the UserProfile database, so we can update summaries.

savedTemplates - Variable in class org.intermine.api.profile.Profile

savedTimes - Variable in class org.intermine.dataloader.HintingFetcher

SaveFromIdsToBagAction - Class in org.intermine.web.struts

Saves selected items with InterMine ids and a Type in a new bag or combines with existing bag.

SaveFromIdsToBagAction() - Constructor for class org.intermine.web.struts.SaveFromIdsToBagAction

saveHistory(SavedQuery) - Method in class org.intermine.api.profile.Profile

Save a query to the query history.

saveIndexToDatabase(ObjectStore, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.lucene.KeywordSearch

writes index and associated directory to the database using the metadatamanager.

saveKeyDefinitions(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager

Save the key definitions, in serialized form, to the specified directory

saveModel(Model, File) - Static method in class org.intermine.modelproduction.MetadataManager

Save a model, in serialized form, to the specified directory

saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable

Set InterMine Object id for the table row

saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable

Used on BagUploadConfirm

savePopulation - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

saveProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager

Synchronise a user's Profile with the backing store

saveProperties(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager

Save the objectstore summary, in serialized form, to the specified directory

saveQueries(Map<? extends String, ? extends PathQuery>) - Method in class org.intermine.api.profile.Profile

Save the map of queries as given to the user's profile, avoiding all possible name collisions.

saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUpdateService

saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUploadService

Save the given queries.

saveQuery(String, SavedQuery) - Method in class org.intermine.api.profile.Profile

Save or update a query.

saveQuery(HttpSession, String, PathQuery, Date) - Static method in class org.intermine.web.logic.session.SessionMethods

Save a clone of a query to the user's Profile.

saveQuery(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods

Save a clone of a query to the user's Profile.

SaveQueryAction - Class in org.intermine.web.struts

Implementation of Action that saves a Query from a session.

SaveQueryAction() - Constructor for class org.intermine.web.struts.SaveQueryAction

SaveQueryForm - Class in org.intermine.web.struts

Form bean to represent the inputs to the query saving action

SaveQueryForm() - Constructor for class org.intermine.web.struts.SaveQueryForm

saveQueryToHistory(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods

Save a clone of a query to the user's Profile history.

saveTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile

Save a template

saveToggleState(String, boolean) - Static method in class org.intermine.dwr.AjaxServices

Saves information, that some element was toggled - displayed or hidden.

saveWithBagValues(Integer, Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag

Save the bag into the userprofile database, along with information about what kinds of values this bag contains.

savingDisabled - Variable in class org.intermine.api.profile.Profile

SAXParser - Class in org.intermine.util

Basic SAX Parser

sb - Variable in class org.intermine.sql.logging.DatabaseWriter

SC_BAD_REQUEST - Static variable in class org.intermine.webservice.server.output.Output

Bad request http status code.

SC_FORBIDDEN - Static variable in class org.intermine.webservice.server.output.Output

Forbidden http status code.

SC_INTERNAL_SERVER_ERROR - Static variable in class org.intermine.webservice.server.output.Output

Internal server http status code.

SC_NO_CONTENT - Static variable in class org.intermine.webservice.server.output.Output

No content http status code.

SC_NOT_FOUND - Static variable in class org.intermine.webservice.server.output.Output

Resource not found http status code.

SC_OK - Static variable in class org.intermine.webservice.server.output.Output

OK http status code.

SC_UNAUTHORIZED - Static variable in class org.intermine.webservice.server.output.Output

Request is legal, but requires authentication, which was either not provided, or failed.

schema - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput

schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask

schemaFile - Variable in class org.intermine.task.BuildDbTask

SchemaListService - Class in org.intermine.webservice.server

Serve up the list of schemata that we have.

SchemaListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SchemaListService

Constructor

SchemaServlet - Class in org.intermine.webservice.server

Returns a requested schema.

SchemaServlet() - Constructor for class org.intermine.webservice.server.SchemaServlet

Scope - Class in org.intermine.api.search

Scope constants.

SCOPES - Static variable in class org.intermine.api.search.Scope

The possible scopes.

score(int) - Method in class org.intermine.sql.precompute.OptimiserCacheLine

Scores this cache line according to how far away the required limit is from the limit used to create the line.

search(String, Collection<String>, String, boolean, boolean) - Method in class org.intermine.api.bag.BagQueryRunner

Given an input list of string identifiers search for corresponding objects.

SEARCH_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key to use to store the search index.

SEARCH_INDEX_DIRECTORY - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key to use to store the search Directory.

SEARCH_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of class that tracks searches

SEARCH_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of table that tracks searches

SearchFilterEngine - Class in org.intermine.api.search

Class filtering web searchables according to the associated tags.

SearchFilterEngine() - Constructor for class org.intermine.api.search.SearchFilterEngine

searchForBag(String, List<String>, String, boolean) - Method in class org.intermine.api.bag.BagQueryRunner

Given an input list of string identifiers search for corresponding objects.

searchItems - Variable in class org.intermine.api.search.SearchRepository

SearchRepository - Class in org.intermine.api.search

The base class for search repositories.

SearchRepository(Profile) - Constructor for class org.intermine.api.search.SearchRepository

Constructor.

SearchResult - Class in org.intermine.api.search

A single item in a set or returned results formed by searching the web-searchable indices with Lucene.

SearchResults - Class in org.intermine.api.search

Representations of Lucene search results over the web-searchable data of the user-profile and the mechanisms for generating a set of such results.

SearchTarget - Class in org.intermine.api.search

An object for encapsulating the scope and type of object requested from a Lucene search of the user profile web searchable items.

SearchTarget(String, String) - Constructor for class org.intermine.api.search.SearchTarget

Constructor.

SEARCHTRACK - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding

label for XML

SearchTrackBinding - Class in org.intermine.api.tracker.xml

SEARCHTRACKS - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding

label for XML

SearchUtils - Class in org.intermine.web.search

The bits of the search infrastructure that belong in the web-package because they have view dependent logic.

seenBrokenOneToMany - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

select - Variable in class org.intermine.sql.query.Query

select(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction

Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).

selectable - Variable in class org.intermine.api.results.Column

selectAll(int, String) - Static method in class org.intermine.dwr.AjaxServices

Select all the elements in a PagedTable

selected - Variable in class org.intermine.web.struts.ModifyTemplateForm

selectedBags - Variable in class org.intermine.web.struts.ModifyBagForm

selectedElements - Variable in class org.intermine.web.struts.ModifyBagDetailsForm

selectedIdsIterator() - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Return an Iterator over the selected Ids

selectedObjects - Variable in class org.intermine.web.struts.SaveBagForm

selectedQueries - Variable in class org.intermine.web.struts.ModifyQueryForm

selectEncoding(ServletRequest) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter

Select an appropriate character encoding to be used, based on the characteristics of the current request and/or filter initialization parameters.

selectId(String, String, String) - Static method in class org.intermine.dwr.AjaxServices

Add an ID to the PagedTable selection

selectId(Integer, int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Add an object id and its field value that has been selected in the table.

SelectValue - Class in org.intermine.sql.query

Represents an AbstractValue with an alias, suitable for use in the SELECT portion of an SQL query.

SelectValue(AbstractValue, String) - Constructor for class org.intermine.sql.query.SelectValue

Construct a new SelectValue.

sendFareWell(String, String) - Method in class org.intermine.util.Emailer

Bid a user farewell from the system.

SensibleByteArrayOutputStream - Class in org.intermine.util

A subclass of ByteArrayOutputStream that behaves a little more sensibly when handling large writes followed by small writes.

SensibleByteArrayOutputStream() - Constructor for class org.intermine.util.SensibleByteArrayOutputStream

SensibleByteArrayOutputStream(int) - Constructor for class org.intermine.util.SensibleByteArrayOutputStream

SEPARATOR - Static variable in class org.intermine.api.tag.TagNames

Tag separator.

seqClsName - Variable in class org.intermine.bio.task.GFF3ConverterTask

seqDataSourceName - Variable in class org.intermine.bio.task.GFF3ConverterTask

sequence - Variable in class org.intermine.objectstore.query.ResultsBatches

SEQUENCE_IGNORE - Static variable in interface org.intermine.objectstore.ObjectStore

Object representing no fail-fast concurrency checks required.

SEQUENCE_MULTIPLE - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

sequenceBase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

sequenceKeys - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

sequenceNumber - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl

sequenceOffset - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

SequenceOntology - Class in org.intermine.bio.ontology

Helper class for SequenceOntology.

SequenceOntology(String, InputStream) - Constructor for class org.intermine.bio.ontology.SequenceOntology

Constructor.

SequenceOntologyFactory - Class in org.intermine.bio.ontology

Class in charge of making sequence ontology objects

SequenceProcessor - Class in org.intermine.bio.dataconversion

A processor for the chado sequence module.

SequenceProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.SequenceProcessor

Create a new SequenceProcessor

SequenceService - Class in org.intermine.webservice.server.clob

A service to provide access to substrings of ClobAccess data.

SequenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.clob.SequenceService

sequential - Variable in class org.intermine.objectstore.query.Results

SERIAL_NUMBER - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store the serial number identifying the production db

SERIAL_SEQUENCE_NAME - Static variable in class org.intermine.task.BuildDbTask

serialize(Properties) - Static method in class org.intermine.util.PropertiesUtil

Serialize properties to a string suitable for a subsequent load()

serveToken(DeletionToken) - Method in class org.intermine.webservice.server.user.NewDeletionTokenService

Serve a token to the outside world.

Service - Class in org.intermine.webservice.client.core

This class provides the base level common functionality required to access any InterMine service.

Service(String, String, String) - Constructor for class org.intermine.webservice.client.core.Service

Constructor.

service(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.WebService

Starting method of web service.

SERVICE_FAILED_MSG - Static variable in class org.intermine.webservice.server.WebServiceConstants

Error message returned in case of unexpected service failure.

serviced - Static variable in class org.intermine.objectstore.query.PrefetchManager

Set of requests currently being serviced.

ServiceException - Exception in org.intermine.webservice.client.exceptions

ServiceException is a base class for all service exceptions.

ServiceException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException

ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException

ServiceException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException

ServiceException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException

Exception is filled in with some detailed information from response.

ServiceException - Exception in org.intermine.webservice.server.exceptions

ServiceException is a base class for all service exceptions.

ServiceException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceException(String, Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceException(Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException

ServiceFactory - Class in org.intermine.webservice.client.core

The Class that should be used for creating services.

ServiceFactory(String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory

Construct a service factory with a default application name.

ServiceFactory(String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory

Construct a factory for gaining access to specific resources.

ServiceFactory(String, String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory

Deprecated.

This method causes username and password information to be insecurely transmitted over HTTP connections. Use the token authentication mechanism instead.

ServiceForbiddenException - Exception in org.intermine.webservice.client.exceptions

The ServiceForbiddenException is thrown by a service when an attempt is made to service that is disabled.

ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException

ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException

ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException

ServiceForbiddenException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException

ServiceForbiddenException - Exception in org.intermine.webservice.server.exceptions

The ServiceForbiddenException is thrown by a service when an attempt is made to service that is disabled.

ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException

ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException

ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException

ServiceListingHandler - Class in org.intermine.webservice.server

ServiceListingHandler() - Constructor for class org.intermine.webservice.server.ServiceListingHandler

ServicesListingsServlet - Class in org.intermine.webservice.server

Provide a list of all the services available at this mine.

ServicesListingsServlet() - Constructor for class org.intermine.webservice.server.ServicesListingsServlet

serviceThreads - Static variable in class org.intermine.objectstore.query.PrefetchManager

ServiceUnavailableException - Exception in org.intermine.webservice.client.exceptions

The ServiceUnavailableException is thrown when an exception occurs that is temporary, the user should try it again.

ServiceUnavailableException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException

ServiceUnavailableException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException

ServiceUnavailableException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException

ServiceUnavailableException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException

SessionActivationListener - Class in org.intermine.web.logic.session

Added to each session to monitor activation events.

SessionActivationListener() - Constructor for class org.intermine.web.logic.session.SessionActivationListener

sessionCreated(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener

sessionDestroyed(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener

sessionDidActivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener

Called after a session is unserialised.

sessionIdentifier - Variable in class org.intermine.api.tracker.track.TrackAbstract

SessionlessRequest - Class in org.intermine.webservice.server.core

SessionlessRequest(HttpServletRequest) - Constructor for class org.intermine.webservice.server.core.SessionlessRequest

Construct a request by wrapping the given request.

SessionListener - Class in org.intermine.web.logic.session

Perform InterMine-specific actions when a Session is constructed or destroyed

SessionListener() - Constructor for class org.intermine.web.logic.session.SessionListener

SessionMethods - Class in org.intermine.web.logic.session

Business logic that interacts with session data.

SessionService - Class in org.intermine.webservice.server

Open a new 24-hour session.

SessionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SessionService

sessionWillPassivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener

Called just before serialising to disk.

set(int, boolean) - Method in class org.intermine.util.IntPresentSet

Adds the given int to the set.

set(int, Object) - Method in class org.intermine.webservice.client.results.ResultRowList

setAccepted(Boolean) - Method in class org.intermine.api.bag.SharingInvite

setAccessions(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setAction(String) - Method in class org.intermine.web.struts.WidgetForm

setActionType(String) - Method in class org.intermine.web.struts.TemplateSettingsForm

setAdditionsFile(File) - Method in class org.intermine.task.ModelMergerTask

The file containing model additions.

setAdditionsFiles(List<File>) - Method in class org.intermine.task.ModelMergerTask

The files containing model additions.

setAlias(String) - Method in class org.intermine.sql.query.AbstractTable

Sets the alias for this AbstractTable object.

setAlias(String) - Method in class org.intermine.task.CreateIndexesTask

Set the ObjectStore alias.

setAlias(String) - Method in class org.intermine.task.DropPrecomputedTablesTask

Set the ObjectStore alias

setAlias(String) - Method in class org.intermine.task.PrecomputeTask

Set the ObjectStore alias.

setAlias(String) - Method in class org.intermine.task.RunIqlQueryTask

Set the ObjectStore alias.

setAlias(String) - Method in class org.intermine.task.SummariseObjectStoreTask

Set the ObjectStore alias

setAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set the ObjectStore alias

setAllowduplicates(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Toggle whether or not to allow duplicate sequences

setAllSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Select a whole column.

setAllSources(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the list of data sources present in the project.xml, for the purposes of verifying the priorities properties file.

setAPI(InterMineAPI) - Method in class org.intermine.api.template.ApiTemplate

Only used on export so we can get the tags related to this template.

setApiKey(String) - Method in class org.intermine.api.profile.Profile

Set the API token for this user, and save it in the backing DB.

setAppendConfig(Boolean) - Method in class org.intermine.web.logic.config.HeaderConfigTitle

Set whether to append config from parent

setApplicationName(String) - Method in class org.intermine.webservice.client.core.ServiceFactory

Set the application name used to identify your requests to the server

setAspectDisplayers(Map<String, List<Displayer>>) - Method in class org.intermine.web.logic.config.Type

setAspects(String) - Method in class org.intermine.web.logic.config.Displayer

Set the aspects of this displayer

setAspects(ServletContext, Map<String, Aspect>) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the Map of aspects.

setAttribute(Integer, String, String) - Method in class org.intermine.bio.dataconversion.ChadoProcessor

Set an attribute in an Item by creating an Attribute object and storing it.

setAttribute(String, Object) - Static method in class org.intermine.web.context.InterMineContext

Set an attribute of the context.

setAttribute(String, String) - Method in class org.intermine.xml.full.Item

Add an attribute to this item.

setAttributeIndexes(boolean) - Method in class org.intermine.task.CreateIndexesTask

Set the attributeIndexes flag.

setAttributeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of attributeOp

setAttributeOps(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm

Set the attribute ops

setAttributeOps(String, String) - Method in class org.intermine.web.struts.TemplateForm

Set an attribute op

setAttributeOptions(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of attributeOptions

setAttributeToEmptyString(String) - Method in class org.intermine.xml.full.Item

Add an attribute to this item and set it to the empty string.

setAttributeValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of attributeValue

setAttributeValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm

Set the attribute values

setAttributeValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm

Set an attribute value

setAuthentication(String, String) - Method in class org.intermine.webservice.client.core.Service

Deprecated.

Use token based authentication instead (Service.setAuthentication(String) as this method will cause your user name and password to be transmitted insecurely across HTTP connections.

setAuthentication(String) - Method in class org.intermine.webservice.client.core.Service

Set the token to be used for authentication.

setAuthToken(String) - Method in interface org.intermine.webservice.client.core.Request

Set the authentication token for the request

setAuthToken(String) - Method in class org.intermine.webservice.client.core.RequestImpl

setAutoCompleter(ServletContext, AutoCompleter) - Static method in class org.intermine.web.logic.session.SessionMethods

Set the AutoCompleter into the ServletContext.

setBag(InterMineBag) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setBag(String, Object) - Method in class org.intermine.web.struts.TemplateForm

Set the bag name.

setBagName(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

name of bag that this widget is using.

setBagName(String) - Method in class org.intermine.web.struts.FindInListForm

setBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Set the value of bagName

setBagName(String) - Method in class org.intermine.web.struts.WidgetForm

name of bag that this widget is using.

setBagOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of bagOp

setBagOp(String, String) - Method in class org.intermine.web.struts.TemplateForm

Set bag operation.

setBagSelected(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint

Set if the bag is selected, used by the method isBagSelected that returns true, even if the constraint is an attribute constraint

setBagTableNames(Map<Object, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

setBagType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setBagType(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Set the bag type

setBagType(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setBagType(String) - Method in class org.intermine.web.struts.WidgetForm

setBagValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of bagValue

setBaseLink(String) - Method in class org.intermine.web.tags.table.NavigationBarTag

setBatchSize(int) - Method in class org.intermine.api.query.PathQueryExecutor

Sets batch size.

setBatchSize(int) - Method in interface org.intermine.objectstore.proxy.LazyCollection

Sets the number of rows requested from the ObjectStore whenever an execute call is made

setBatchSize(int) - Method in class org.intermine.objectstore.proxy.ProxyCollection

Sets the number of rows requested from the ObjectStore whenever an execute call is made

setBatchSize(int) - Method in class org.intermine.objectstore.query.Results

Sets the number of rows requested from the ObjectStore whenever an execute call is made

setBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches

Sets the number of rows requested from the ObjectStore whenever an execute call is made

setBatchWriter(BatchWriter) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Allows the changing of the BatchWriter that this ObjectStoreWriter uses.

setBatchWriter(BatchWriter) - Method in class org.intermine.sql.writebatch.Batch

Changes the BatchWriter for a new one.

setBiogridOrganisms(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter

Sets the list of taxonIds that should be imported if using split input files.

setBlockCount(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setBlockCount(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord

setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord

setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord

setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord

setBuildDir(String) - Method in class org.intermine.web.task.IssueTokenTask

Bean-style setter, as per the ant spec.

setCacheDirName(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Set the cache file name

setCaseSensitive(boolean) - Method in class org.intermine.web.struts.BuildBagForm

setCategories(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the aspect categories into the servlet context.

setCategoryPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

SetCharacterEncodingFilter - Class in org.intermine.web.filters

Example filter that sets the character encoding to be used in parsing the incoming request, either unconditionally or only if the client did not specify a character encoding.

SetCharacterEncodingFilter() - Constructor for class org.intermine.web.filters.SetCharacterEncodingFilter

setCharSet(String) - Method in class org.intermine.webservice.client.core.ContentType

Sets character set of this content type.

setChildTermId(String) - Method in class org.intermine.bio.ontology.OboRelation

setChrom(String) - Method in class org.intermine.bio.io.bed.BEDRecord

setChrom(String) - Method in class org.intermine.bio.io.gaf.GAFRecord

setChromEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setChromEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setChromosomeLocationsAndLengths() - Method in class org.intermine.bio.postprocess.CalculateLocations

For each SequenceFeature, if it has a Location on a Chromosome, set the SequenceFeature.chromosomeLocation reference to be that Location and set the length field of the SequenceFeature to chromosomeLocation.end - chromosomeLocation.start + 1

setChromStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setChromStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setClassAttribute(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

The attribute of the class created to set with the identifying field.

setClassConfig(Type) - Method in class org.intermine.web.logic.config.FieldConfig

setClassDescriptor(String) - Method in class org.intermine.xml.full.Item

Set the classDescriptor attribute to be the ClassDescriptor for the given className in the Model set by setModel().

setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.bag.operations.BagOperation

setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setClassLoader(ClassLoader) - Method in class org.intermine.web.task.CreateSearchIndexTask

Set the class loader

setClassName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

The class name to use for objects created during load.

setClassName(String) - Method in class org.intermine.task.AnalyseDbTask

Set an optional class name, must also set model name

setClassName(String) - Method in class org.intermine.task.StaticMethodTask

Set class name on which to call static method.

setClassName(String) - Method in class org.intermine.web.logic.config.TableExportConfig

Set the className of this TableExportConfig

setClassName(String) - Method in class org.intermine.web.logic.config.Type

Set the unqualified class name for this Type (from fully-qualified)

setClassName(String) - Method in class org.intermine.web.logic.results.InlineResultsTableRow

setClassName(String) - Method in class org.intermine.web.struts.QueryClassSelectForm

Set the class name

setClassName(String) - Method in class org.intermine.xml.full.Item

Set the class of this item.

setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable

Set a class name on table row

setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable

Set a class name on table row, used for type safety as overriden on BagUploadConfirm

setClsName(String) - Method in class org.intermine.task.DBConverterTask

Set the source specific subclass of FileConverter to run

setClsName(String) - Method in class org.intermine.task.DirectoryConverterTask

Set the source specific subclass of DirectoryConverter to run

setClsName(String) - Method in class org.intermine.task.FileConverterTask

Set the source specific subclass of FileConverter to run

setClsName(String) - Method in class org.intermine.task.PostProcessorTask

Set the name of the PostProcessor sub-class to load to do the postprocessing.

setCode(String) - Method in class org.intermine.web.logic.query.DisplayConstraint

setCode(String) - Method in class org.intermine.web.logic.template.ConstraintInput

setCollection(String, List<String>) - Method in class org.intermine.xml.full.Item

Set a collection.

setColumnId(String) - Method in class org.intermine.api.results.Column

setColumnNames(List<String>) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Set the column names

setColumnNames(List<String>) - Method in class org.intermine.web.tags.table.TableTag

setColumnTitle(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setComment(String) - Method in class org.intermine.template.TemplateQuery

Set the private comment for this template.

setComment(String) - Method in class org.intermine.web.struts.TemplateSettingsForm

Set the comment

setCommentEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setComments(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setCommentType(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

Creates a new temporary object to hold the type and later the publications for this comment.

setComplete(long) - Method in class org.intermine.objectstore.query.ResultsInfo

Sets the estimated amount of time taken to produce the entire set of results.

setComputeTotalCount(boolean) - Method in class org.intermine.webservice.server.query.result.QueryResultInput

Sets true if compute total count of all available results.

setConfigFile(File) - Method in class org.intermine.task.AcceptanceTestTask

Set the File to read configuration from

setConfigFileName(String) - Method in class org.intermine.task.SummariseObjectStoreTask

Set the name of the Properties file containing the names of the classes and fields to summarise.

setConfigurationFile(File) - Method in class org.intermine.task.TSVFileReaderTask

Set the configuration file to use.

setConnectField(String) - Method in class org.intermine.api.bag.BagQueryConfig

Set the connecting field for adding an extra constraint to bag queries.

setConnectionTimeout(int) - Method in class org.intermine.webservice.client.core.Service

Sets connection timeout.

setConstrainField(String) - Method in class org.intermine.api.bag.BagQueryConfig

Set the field to constrain when making an extra constraint.

setConstraint(TemplateQuery, TemplateValue) - Static method in class org.intermine.api.template.TemplatePopulator

Set the value for a constraint in the template query with the given TemplateValue.

setConstraint(Constraint) - Method in class org.intermine.objectstore.query.Query

Constrain this Query using either a single constraint or a set of constraints

setConstraint(Constraint) - Method in interface org.intermine.objectstore.query.Queryable

Sets the additional constraint.

setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Sets the additional constraint.

setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression

Sets the additional constraint.

setConstraintDescription(PathConstraint, String) - Method in class org.intermine.template.TemplateQuery

Sets the description for a constraint.

setConstraintLogic(String) - Static method in class org.intermine.dwr.AjaxServices

Set the constraint logic on a query to be the given expression.

setConstraintLogic(String) - Method in class org.intermine.pathquery.PathQuery

Sets the current constraint logic.

setConstraintOp(ConstraintOp) - Method in class org.intermine.web.logic.template.ConstraintInput

Sets constraint operation.

setConstraints(Map<String, List<ConstraintInput>>) - Method in class org.intermine.web.logic.template.TemplateResultInput

Sets constraints.

setConstraints(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setConstraintsForView(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setContent(String) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig

Set the content of the widget.

setContent(File) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content for this creation request as coming from a file on the file-system.

setContent(InputStream) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content for this creation request as coming from an InputStream.

setContent(Collection<String>) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content for this request as coming from a set of strings, with each string representing one identifier.

setContent(String...) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content for this request as coming from a set of strings, with each string representing one identifier.

setContent(String) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content as coming from a string.

setContent(PathQuery) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo

Set the content for this request as a query to run to find objects with.

setContentType(ContentType) - Method in interface org.intermine.webservice.client.core.Request

setContentType(ContentType) - Method in class org.intermine.webservice.client.core.RequestImpl

setConverter(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

setConverter(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the converter

setCorrection(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

setCorrectionCoefficient(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setCount(int) - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor

Set the query count/size.

setCountFormat() - Method in class org.intermine.webservice.client.core.RequestImpl

Set the format as count format.

setCreategenes(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Toggle whether or not to create genes and protein/gene associations.

setCreatego(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Toggle whether or not to import GO data

setCreateinterpro(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Deprecated.

The UniProt data source does not create interpro domains any longer. Please use the InterPro data source instead.

setCreaterelations(String) - Method in class org.intermine.bio.dataconversion.OboConverter

Set to false to prevent storing OntologyRelation objects that include the relationship types between terms.

setCSVContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets comma separated values content type.

setCSVHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for comma separated values output.

setCurrentFile(File) - Method in class org.intermine.dataconversion.FileConverter

Set the current File that is being processed.

setCurrentMapFromCurrentArray(ResultElement) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Finds the object we should be dealing with by getting it from the current array.

setCurrentMapFromCurrentArray() - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Sets the current map to work with by getting the last one from the current array.

setCurrentPage(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag

setCustomContentType(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets content type to the parameter specified

setCustomTypeHeader(HttpServletResponse, String, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for a custom content type.

setDatabase(String) - Method in class org.intermine.task.AcceptanceTestTask

Set the database alias

setDatabase(String) - Method in class org.intermine.task.GrantTask

Set the database alias

setDataDir(String) - Method in class org.intermine.task.DirectoryConverterTask

Set the dataDir.

setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter

Update the dataset reference Id.

setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioStoreHook

Update the dataset reference Id.

setDatasetRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setDataSets(Model, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook

Do the work of processItem() by setting DataSet and DataSource references and collections on the given Item.

setDataSetTitle(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

If a value is specified this title will used when a DataSet is created.

setDataSetTitle(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the dataSetTitle

setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter

Set the name of the DataSource Item to create for this converter.

setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Datasource for any bioentities created

setDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the dataSourceName

setDate(Date) - Method in class org.intermine.api.profile.InterMineBag

Sets date when bag was created.

setDb(Database) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

setDbAlias(String) - Method in class org.intermine.task.DBConverterTask

Set the Database to read from

setDbrefs(Map<String, Set<String>>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setDefaultValue(String, String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser

Set a parameter default.

setDeleteTracks(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm

Set the deleteTracks flag.

setDescr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setDescription(String) - Method in class org.intermine.api.profile.InterMineBag

setDescription(String) - Method in class org.intermine.api.template.ApiTemplate

setDescription(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

setDescription(String) - Method in class org.intermine.bio.ontology.OboTerm

Set the term description.

setDescription(String, String) - Method in class org.intermine.pathquery.PathQuery

Sets the description for a given path.

setDescription(String) - Method in class org.intermine.pathquery.PathQuery

Sets the description for this PathQuery.

setDescription(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setDescription(String) - Method in class org.intermine.web.struts.TemplateSettingsForm

Set the description

setDescriptor(FieldDescriptor) - Method in class org.intermine.web.logic.results.InlineList

Set FieldDescriptor so we can work with placements

setDestDir(File) - Method in class org.intermine.task.ModelOutputTask

Sets the directory that output should be written to.

setDestDir(File) - Method in class org.intermine.task.RetrieveMetadataTask

Sets the destination directory

setDestFile(File) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask

Sets the file to which the data should be written.

setDirect(boolean) - Method in class org.intermine.bio.ontology.OboRelation

setDirectChildren(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm

Set the direct children of this term.

setDirectParents(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm

Set the direct parents of this term.

setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Sets the disableResultsCache configuration option.

setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Sets the disableResultsCache configuration option.

setDisease(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder

setDisplayer(String) - Method in class org.intermine.web.logic.config.FieldConfig

Set the displayer

setDisplayFields(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setDistinct(boolean) - Method in class org.intermine.objectstore.query.Query

Set the value of the distinct property, which determines whether duplicates are permitted in the results returned by this Query

setDistinct(boolean) - Method in class org.intermine.sql.query.Query

Sets the distinct status of this query.

setDoGzip(boolean) - Method in class org.intermine.web.struts.TableExportForm

Set whether the output should be GZIPped.

setDomain(String) - Method in class org.intermine.api.beans.PartnerLink

setDomainLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Set the value of domainLabel

setDomains(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setDoNotTruncate(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

If set to true, don't truncate long fields or put in a [View all...] link in the object details page.

setDontCreateLocations(boolean) - Method in class org.intermine.bio.dataconversion.GFF3Converter

Set the dontCreateLocations flag

setDontCreateLocations(boolean) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the dontCreateLocations flag, the default is false - create locations.

setDuplicate(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setEditable(PathConstraint, boolean) - Method in class org.intermine.template.TemplateQuery

Sets a constraint to be editable or not.

seteditable(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setEditable(boolean) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the editable flag (when building a template).

setEditableConstraints(List<PathConstraint>) - Method in class org.intermine.template.TemplateQuery

Sets the list of editable constraints to exactly that provided, in the given order.

setEditableInTemplate(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint

setEdited(boolean) - Method in class org.intermine.template.TemplateQuery

Set the query as being edited.

setEditingConstraintCode(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the code of an existing constraint that is being edited.

setEmail(String) - Method in class org.intermine.web.task.IssueTokenTask

Bean-style setter, as per the ant spec.

setEnd(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Set end value

setEnrich(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setEnrichIdentifier(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setEnsemblDb(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask

Sets the value of ensemblDb

setEnsemblPrefix(String) - Method in class org.intermine.bio.util.OrganismData

setEof(HintingFetcher) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Sets the equivalent object fetcher.

setErr(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask

Set the error handler

setError(String, int) - Method in class org.intermine.webservice.server.output.Output

Sets the error message

setErrorCorrection(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setErrorCorrection(String) - Method in class org.intermine.web.struts.WidgetForm

setErrorOnInitialiser(ServletContext, Map<String, String>) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the blocking error codes into the servlet context.

setEscapeXml(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

If set to true, don't escape the field value on object details page.

setEstimatedRows(long) - Method in class org.intermine.sql.query.ExplainResult

Use this to provide the object with a "better" estimate of the number of rows in the results of this Query.

setExcludeList(String) - Method in class org.intermine.task.ConverterTask

Sets the list of classes to NOT try and convert

setExistingBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Sets the value of existingBagName

setExistingBagName(String) - Method in class org.intermine.web.struts.SaveBagForm

Sets the value of existingBagName

setExpiry(String) - Method in class org.intermine.web.task.IssueTokenTask

Bean-style setter, as per the ant spec.

setExplain(boolean) - Method in class org.intermine.sql.query.Query

Sets the explain status of this query.

setExportField(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setExporttype(String) - Method in class org.intermine.web.struts.WidgetForm

setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setExternalLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setExternalLinkLabel(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setExtraAttribute(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

setExtraConstraintClassName(String) - Method in class org.intermine.api.bag.BagQueryConfig

Set the class name of extra constraint to use in BagQuery objects using this config object.

setExtraFieldValue(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Set the extra field value

setExtraFieldValue(String) - Method in class org.intermine.web.struts.BuildBagForm

Set the extra field value.

setExtraFieldValue(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm

setExtraThreads(int) - Method in class org.intermine.task.CreateIndexesTask

Set the number of extra worker threads.

setExtraValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput

Sets extra value

setExtraValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of extraValue

setExtraValue(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput

An extra value, such as an organism, for use in lookup constraints.

setExtraValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm

Sets the extra values

setExtraValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm

Set an extra value

setFactory(ServiceFactory) - Method in class org.intermine.webservice.client.core.Service

Set the ServiceFactory this service can use to access other services.

setFastaTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Set the Taxon Id of the Organism we are loading.

setFavourite(String, String, boolean) - Method in class org.intermine.dwr.AjaxServices

Creates a favourite Tag for the given templateName

setFeature(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set the feature item for this record.

setFetchFields(boolean, Set<FieldDescriptor>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

Sets variables which determines which fields are prefetched.

setField(Object) - Method in class org.intermine.api.results.ResultElement

Set the field value

SetFieldConfigAction - Class in org.intermine.bio.chado.config

An action that sets an attribute in a new Item.

SetFieldConfigAction(String) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction

Create a new SetFieldConfigAction that sets the given field.

SetFieldConfigAction(String, Pattern) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction

Create a new SetFieldConfigAction that sets the given field.

setFieldExporter(String) - Method in class org.intermine.web.logic.config.FieldConfig

Set the class name of the FieldExporter to use when this field is viewed.

setFieldExpr(String) - Method in class org.intermine.web.logic.config.FieldConfig

Set the JSTL expression for this field which will be evaluated in the request context when the JSP is viewed.

setFieldToAlias(FromElement, Map<String, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State

setFieldValue(String, Object) - Method in class org.intermine.objectstore.proxy.ProxyReference

setFieldValue(Object, String, Object) - Static method in class org.intermine.util.DynamicUtil

Sets the value of a public or protected Field of an Object given the field name.

setFile(String) - Method in class org.intermine.bio.task.OboConverterTask

Set the input file name

setFile(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set a file name to load from

setFile(String) - Method in class org.intermine.task.FullXmlConverterTask

Set a file name to load from

setFileArray(File[]) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Directly set the array of files to read from.

setFileName(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the content disposition filename.

setFileName(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Set the name of the file to write to.

setFileName(String) - Method in class org.intermine.web.task.ProfileReadTask

Set the name of the file to read from.

setFileName(String) - Method in class org.intermine.web.task.ProfileWriteTask

Set the name of the file to write to.

setFileName(String) - Method in class org.intermine.web.task.TemplateTrackReadTask

Set the name of the file to read from.

setFileName(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask

Set the name of the file to write to.

setFilter(String) - Method in class org.intermine.web.logic.widget.EnrichmentWidget

setFilter(String) - Method in class org.intermine.web.logic.widget.GraphWidget

setFilter(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setFilter(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

setFilterLabel(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setFilterLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setFilters(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setFilters(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr

builds, runs query.

setFormat(String) - Method in class org.intermine.web.struts.CSVExportForm

Set the format.

setFormat(String) - Method in class org.intermine.webservice.client.core.RequestImpl

Set the format for the request.

setFormat(Format) - Method in class org.intermine.webservice.server.WebService

For very picky services, you can just set it yourself, and say "s****w you requester".

setFormFile(FormFile) - Method in class org.intermine.web.struts.BuildBagForm

Set the FormFile.

setFormFile(FormFile) - Method in class org.intermine.web.struts.ImportXMLForm

Set the FormFile.

setFragment(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry

dev can configure converter to load these or not.

setFull(boolean) - Method in class org.intermine.task.AnalyseDbTask

Set true if a VACUUM FULL ANALYSE required

setGaff(String) - Method in class org.intermine.bio.dataconversion.GoConverter

Sets the file format for the GAF. 2.0 is the default.

setGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

set the gene designation for this taxon. can be NULL

setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor

Method to set the source for gene for modencode datasources it will add the title

setGeneSource(Integer, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

to set source field if in the model (modmine)

setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

set the source field for modENCODE gene

setGlobalSearchRepository(ServletContext, SearchRepository) - Static method in class org.intermine.web.logic.session.SessionMethods

Set the SearchRepository for global (public) objects in the servlet context.

setGOTerms(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setGraphType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setGzippedContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets gzip content type ("application/octet-stream")

setGzippedHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for gzipped output.

setHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the name of GFF3RecordHandler class to use when processing.

setHeader(String, String) - Method in interface org.intermine.webservice.client.core.Request

Sets a request header.

setHeader(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl

Sets a request header.

setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Output

Sets header attributes that are displayed for example in xml header.

setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.StreamedOutput

Sets header attributes that are displayed for example in xml header.

setHeaderAttributes(String) - Method in class org.intermine.webservice.server.query.QueryToListService

Sets the header attributes map on the current output object.

setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.QueryResultService

Set the header attributes of the output based on the values of the PathQuery

setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.TableRowService

setHide(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

If set to true, do not display field on report page.

setHighlight(String) - Method in class org.intermine.web.struts.WidgetForm

setHTMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets HTML content type.

setIconImage(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the icon Image

setId(String) - Method in class org.intermine.bio.io.gff3.GFF3Record

Set the Id of this GFF3Record.

setId(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition

setId(Integer) - Method in interface org.intermine.model.InterMineObject

Setter for the ID field.

setId(Integer) - Method in class org.intermine.objectstore.proxy.ProxyReference

Sets the ID value

setId(String) - Method in class org.intermine.web.logic.config.TableExportConfig

Set the id of this TableExportConfig

setId(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setId(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Sets element id.

setIdentifier(String) - Method in class org.intermine.api.beans.ObjectDetails

setIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder

setIdentifier(String) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Set identifier

setIdentifier(String) - Method in class org.intermine.xml.full.Item

Set the identifier of this item.

setIdentifierMap(Map<?, ?>) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set the Map of GFF identifiers to Item identifier.

setIdentifierName(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

setIdSuffix(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Set the suffix to add to identifiers from the FASTA file when creating BioEnitys.

setIgnore(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set a comma separated list of template names to ignore - i.e. not precompute.

setIgnoreDuplicates(boolean) - Method in interface org.intermine.dataloader.IntegrationWriter

Tell this IntegrationWriter whether to ignore duplicate objects from the same source.

setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Tell this IntegrationWriter whether to ignore duplicate objects from the same source.

setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the value of ignoreDuplicates for the IntegrationWriter.

setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set the value of ignoreDuplicates for the IntegrationWriter

setIgnoreDuplicates(boolean) - Method in class org.intermine.task.DirectDataLoaderTask

Set the value of ignoreDuplicates for the IntegrationWriter

setImage(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink

Set

setImmutable() - Method in class org.intermine.objectstore.query.Results

Tells this Results object that it is being put into a cache, so it needs to be made immutable to prevent threads stomping on each other and changing settings.

setImplementations(String) - Method in class org.intermine.xml.full.Item

Set the "implements" of this item.

setIncludeHeaders(boolean) - Method in class org.intermine.web.struts.TableExportForm

Set the includeHeaders flag.

setIndex(int) - Method in class org.intermine.api.results.Column

Sets the value of index

setInputModelFile(File) - Method in class org.intermine.task.ModelMergerTask

Set the model to add additions to.

setIntactOrganisms(String) - Method in class org.intermine.bio.dataconversion.PsiConverter

Sets the list of taxonIds that should be imported if using split input files.

setIntegrationWriter(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the IntegrationWriter.

setIntegrationWriter(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set the IntegrationWriter.

setIntegrationWriterAlias(String) - Method in class org.intermine.task.DirectDataLoaderTask

Set the IntegrationWriter.

setInterMineAPI(ServletContext, InterMineAPI) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the InterMineAPI in the servlet context.

setIntroText(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the introduction text

setInvite(String) - Method in class org.intermine.web.struts.InvitationForm

setIsoform(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setItemRgb(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setItemRgb(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setJavaClass(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set the Java class name of the controller for this displayer.

setJoinType(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

setJSONContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the content type to "application/json"

setJSONFormat() - Method in class org.intermine.webservice.client.core.RequestImpl

Set the format as JSON-Object format.

setJSONHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the response header and content type for json output

setJSONHeader(HttpServletResponse, String, boolean) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the response header and content type for json output

setJSONPContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the content type to "text/javascript"

setJSONPHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the response header and content type for jsonp output

setJSONRowsFormat() - Method in class org.intermine.webservice.client.core.RequestImpl

Set the format as JSON-Rows format.

setJSONSchemaContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets the content type to "application/schema+json"

setJSONSchemaHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Set the header for a JSON-schema response.

setJspName(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set the name of the JSP associated with this displayer.

setKeggOrganisms(String) - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter

Sets the list of taxonIds that should be imported

setKeyFieldNames(List<String>) - Method in class org.intermine.api.profile.InterMineBag

Set the keyFieldNames

setKeystoreFile(String) - Method in class org.intermine.web.task.KeyStoreTask

Bean-style setter for keystoreFile, as per ant spec.

setKeyToRetreive(String) - Method in class org.intermine.task.RetrieveMetadataTask

Set a key to retrieve from database.

setKeywords(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setLabel(String) - Method in class org.intermine.web.logic.config.FieldConfig

Set the label for this field-configuration.

setLabel(String) - Method in class org.intermine.web.logic.config.Type

Set the label property.

setLabel(String) - Method in class org.intermine.web.logic.query.DisplayConstraint

Set the label of the constraint.

setLabel(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setLargeImage(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the webapp relative path to the large image.

setLayout(String) - Method in class org.intermine.web.logic.template.TemplateResultInput

setLayout(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput

setLdr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setLength(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setLimit(int) - Method in class org.intermine.objectstore.query.Query

Sets the LIMIT parameter for this query - note that this is only honoured in a subquery.

setLimit(Integer) - Method in class org.intermine.webservice.server.WebServiceInput

Sets maximum of returned results.

setLimitOffset(int, int) - Method in class org.intermine.sql.query.Query

Sets the LIMIT and OFFSET numbers for this query.

setLineLength(Integer) - Method in class org.intermine.web.logic.config.InlineListConfig

Sets the amount of entries to show based on their total length

setLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setLink(String) - Method in class org.intermine.web.struts.WidgetForm

setLinkFile(File) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

Set the linkFile attribute.

setLinkRedirect(String) - Method in class org.intermine.api.results.ResultElement

setListLeft(String) - Method in class org.intermine.web.struts.ModifyBagForm

setListPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setListRight(String) - Method in class org.intermine.web.struts.ModifyBagForm

setListsButton(String) - Method in class org.intermine.web.struts.ModifyBagForm

setListSize(Integer) - Method in class org.intermine.webservice.server.lists.ListUploadService

Sets the size of the list on the header attributes.

setLoadfragments(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Toggle whether or not to load fragments.

setLoadFullRecord(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Load summary version of Publication record by default.

setLoadtrembl(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Toggle whether or not to load trembl data for all given organisms

setLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set the location item for this record.

setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Allows the log to be set in this objectstore.

setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Not implemented.

setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Sets the logBeforeExecute configuration option.

setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Sets the logBeforeExecute configuration option.

setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Sets the logEverything configuration option.

setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Sets the logEverything configuration option.

setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Sets the logExplains configuration option.

setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Sets the logExplains configuration option.

setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Allows the log table name to be set in this objectstore.

setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Not implemented.

setLoopQueryOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of loopQueryOp

setLoopQueryValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of loopQueryValue

setMailinglist(boolean) - Method in class org.intermine.web.struts.CreateAccountForm

setMainTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle

Set main title(s) path(s) for the object, e.g.: symbol, primaryIdentifier => eve FBgn0000606

setMatchIDs(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Set the encoded match ids.

setMatchOnFirst(boolean) - Method in class org.intermine.api.bag.BagQueryConfig

If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.

setMaterialisedCollection(Collection<E>) - Method in class org.intermine.objectstore.proxy.ProxyCollection

Sets the collection with a new materialised collection.

setMax(int) - Method in class org.intermine.objectstore.query.ResultsInfo

Sets the maximum possible number of rows in the results.

setMax(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setMax(String) - Method in class org.intermine.web.struts.WidgetForm

setMaxCount(int) - Method in class org.intermine.webservice.client.core.RequestImpl

Sets the maximum number of rows returned.

setMaxP(double) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

setMaxQueryParseTime(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Set the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.

setMessage(String) - Method in class org.intermine.web.struts.ContactForm

setMethod(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

terms describe the method used int he experiment, eg two hybrid, etc

setMethod(String) - Method in class org.intermine.task.StaticMethodTask

Name of method to call.

setMin(int) - Method in class org.intermine.objectstore.query.ResultsInfo

Sets the minimum possible number of rows in the results.

setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Set the cutoff value used to decide if a bag should be put in a table.

setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Set the cutoff value used to decide if a bag should be put in a table.

setMineId(Integer) - Method in class org.intermine.webservice.server.lists.ListsServiceInput

Sets Intermine unique object id

setMinRows(int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer

Set the minimum row count for precomputed queries.

setMinRows(Integer) - Method in class org.intermine.task.PrecomputeTask

Set the minimum row count for precomputed queries.

setMinRows(Integer) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set the minimum row count for precomputed queries.

setMissingChromosomeLocations() - Method in class org.intermine.bio.postprocess.CalculateLocations

For each SequenceFeature, if it has a Location on a Chromosome, set the SequenceFeature.chromosomeLocation reference *if* the reference is not already set.

setMode(String) - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Sets the optimiser mode of operation.

setModel(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the name of model to create data in

setModel(Model) - Method in class org.intermine.pathquery.Node

Attach the model.

setModel(String) - Method in class org.intermine.task.AnalyseDbTask

Set model name, must be set if class name specified

setModel(String) - Method in class org.intermine.task.BuildDbTask

Sets the model

setModel(String) - Method in class org.intermine.task.ModelOutputTask

Set the model to be used.

setModel(Model) - Method in class org.intermine.web.logic.query.MetadataNode

setModel(Model) - Method in class org.intermine.xml.full.Item

Set the Model to use when checking calls to the other set methods

setModelName(String) - Method in class org.intermine.task.ConverterTask

Set the target model name

setModelName(String) - Method in class org.intermine.task.StoreMetadataTask

Sets the model name

setMolecularWeight(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setMonkey(String) - Method in class org.intermine.web.struts.ContactForm

setMultiValueAttribute(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of multiValueAttribute, a string representing the values selected by the user separated by a comma.

setMultiValueAttribute(Map<String, String>) - Method in class org.intermine.web.struts.TemplateForm

Set the multivalueattribute

setMultiValueAttribute(String, String) - Method in class org.intermine.web.struts.TemplateForm

Set the multivalueattribute

setMultivalues(List<String>) - Method in class org.intermine.web.logic.template.ConstraintInput

Set multivalues

setMultiValues(Map<String, String[]>) - Method in class org.intermine.web.struts.TemplateForm

Set the multiValues

setMultiValues(String, String[]) - Method in class org.intermine.web.struts.TemplateForm

Set a multiselect attribute value

setName(String) - Method in class org.intermine.api.beans.ObjectDetails

setName(String) - Method in class org.intermine.api.profile.InterMineBag

Set the value of name

setName(String) - Method in class org.intermine.api.template.ApiTemplate

setName(String) - Method in class org.intermine.bio.chado.ChadoCVTerm

Set the name of this term.

setName(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setName(String) - Method in class org.intermine.bio.io.bed.BEDRecord

setName(String) - Method in class org.intermine.bio.io.gaf.GAFRecord

setName(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition

setName(String) - Method in class org.intermine.template.TemplateQuery

Sets the query short name.

setName(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the data set name.

setName(String) - Method in class org.intermine.web.logic.aspects.AspectSource

Set the source name.

setName(String) - Method in class org.intermine.web.logic.template.TemplateResultInput

Sets template name.

setName(String) - Method in class org.intermine.web.struts.ContactForm

setName(String) - Method in class org.intermine.web.struts.TemplateForm

Set the template name.

setName(String) - Method in class org.intermine.web.struts.TemplateSettingsForm

setName(String) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest

Sets the name of the template to be used.

setName(String) - Method in class org.intermine.xml.full.Attribute

Set the name of this field

setName(String) - Method in class org.intermine.xml.full.Reference

Set the name of this field

setName(String) - Method in class org.intermine.xml.full.ReferenceList

Set the name of this field.

setNameSource(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

setNamespace(String) - Method in class org.intermine.bio.ontology.OboTerm

Set the namespace attribute.

setNameSpace(String) - Method in class org.intermine.webservice.server.WebService

Set the default name-space for configuration property look-ups.

setNewBagName(String) - Method in class org.intermine.api.bag.operations.BagOperation

setNewBagName(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Set the bag name.

setNewBagName(String) - Method in class org.intermine.web.struts.ModifyBagForm

Set the new bag name.

setNewBagName(String) - Method in class org.intermine.web.struts.SaveBagForm

Sets the value of newBagName

setNewBagType(String) - Method in class org.intermine.web.struts.TriageBagForm

Set the new bag name.

setNewpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm

The new password

setNewpassword(String) - Method in class org.intermine.web.struts.PasswordResetForm

Sets the value of newpassword.

setNewpassword2(String) - Method in class org.intermine.web.struts.ChangePasswordForm

New password verification

setNewpassword2(String) - Method in class org.intermine.web.struts.PasswordResetForm

Sets the value of newpassword2.

setNextEnabled(boolean) - Method in class org.intermine.web.tags.table.NavigationBarTag

setNoCache(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets that the result must not be cached.

setNoCacheEnforced(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets enforced no-cache headers to completely disable cache for this response.

setNoExplain() - Method in interface org.intermine.objectstore.proxy.LazyCollection

Sets this LazyCollection to bypass the explain check in ObjectStore.execute().

setNoExplain() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Sets this LazyCollection to bypass the explain check in ObjectStore.execute().

setNoExplain() - Method in class org.intermine.objectstore.query.Results

Sets this Results object to bypass the explain check in ObjectStore.execute().

setNoOptimise() - Method in interface org.intermine.objectstore.proxy.LazyCollection

Sets this LazyCollection to bypass the optimiser

setNoOptimise() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Sets this LazyCollection to bypass the optimiser

setNoOptimise() - Method in class org.intermine.objectstore.query.Results

Sets this Results object to bypass the optimiser.

setNoPrefetch() - Method in class org.intermine.objectstore.query.Results

Tells this Results object to never do any background prefetching.

setNoResultsMessage(String) - Method in class org.intermine.web.tags.table.TableTag

setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.HTMLWidget

setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.Widget

setNullConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the null/not null constraint.

setNullConstraint(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm

Set the nullConstraint

setNullConstraint(String, String) - Method in class org.intermine.web.struts.TemplateForm

Set a nullConstraint

setNumberOfMainTitlesToShow(Integer) - Method in class org.intermine.web.logic.config.HeaderConfigTitle

How many main titles to show in the main title

setNumberOpt(String) - Method in class org.intermine.web.struts.WidgetForm

setOAuth2Providers(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods

Set the set of supported OAuth2 providers to use.

setoBJECT(String, ObjectStore) - Method in interface org.intermine.model.InterMineObject

Sets the values of the fields to the values in the given NotXml.

setoBJECT(String[], ObjectStore) - Method in interface org.intermine.model.InterMineObject

Sets the values of the fields to the values in the given split NotXml.

setoBJECT(String, ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference

Sets the values of the fields to the values in the given NotXml.

setoBJECT(String[], ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference

Sets the values of the fields to the values in the given split NotXml.

setObjectId(Integer) - Method in class org.intermine.web.logic.results.InlineResultsTableRow

Set imObj ID for the object (taken from the first valid imObj id for this row)

setObjects(Set<ObjectDetails>) - Method in class org.intermine.api.beans.PartnerLink

setObjectStore(ObjectStore) - Method in class org.intermine.objectstore.translating.Translator

Set this Translator's ObjectStore.

setObjectStore(ObjectStore) - Method in class org.intermine.task.CreateIndexesTask

Set the ObjectStore to use.

setObjectStore(ObjectStore) - Method in class org.intermine.web.task.CreateSearchIndexTask

Set the object store.

setObjectStoreAlias(String) - Method in class org.intermine.web.task.EvictOrphansTask

Bean-style setter so that any can do its stuff.

setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

Sets the value of objectStoreWriter

setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask

Sets the value of objectStoreWriter

setOboRelations(List<OboRelation>) - Method in class org.intermine.bio.dataconversion.OboConverter

setOboTerms(Collection<OboTerm>) - Method in class org.intermine.bio.dataconversion.OboConverter

setObsolete(boolean) - Method in class org.intermine.bio.ontology.OboTerm

Set the obsolete flag for this OboTerm as read from an OBO file.

setOldModelLocation(String) - Method in class org.intermine.web.task.ModelUpdateTask

Set the location of the previous model.

setOldpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm

The old password

setOnClick(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag

setOntologyName(String) - Method in class org.intermine.bio.task.OboConverterTask

Set the name of the ontology

setOntologyPrefix(String) - Method in class org.intermine.bio.dataconversion.OboConverter

The prefix of ontology terms to be processed.

setOpenByDefault(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Set whether this field should be uncollapsed if sectionOnRight is true.

setOpened(boolean) - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Sets new state of disclosure.

setOpenIdProviders(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods

Set the set of supported Open-ID providers to use.

setOperation(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask

Sets the value of operation

setOperationButton(String) - Method in class org.intermine.web.struts.SaveBagForm

setOperator(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the operator, "and" or "or"

setOptions(String) - Method in class org.intermine.web.task.KeyStoreTask

Bean-style setter for optionsFile, as per ant spec.

setOptionsTileName(String) - Method in class org.intermine.web.logic.config.TableExportConfig

Set the optionsTileName of this TableExportConfig

setOrCheckClass(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Set the class, or if one is already set on the map, check that this one is valid for it.

setOrCheckClassAndId(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Sets the basic information (class and objectId) on the jsonMap provided.

setOrCheckId(ResultElement, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator

Set the id, or if one is already set, check that it matches the one on the map.

setOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set organism item, this is global across record handler and final

setOrganisms(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Set the taxon ids to use when creating the Organism Item for the new features.

setOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask

A space separated list of NCBI taxon ids to include in the filter output.

setOrganisms(String) - Method in class org.intermine.bio.postprocess.IntronUtil

Set a comma separated list of taxon ids to create introns for.

setOrgTaxonId(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the organism taxon id

setOriginalConstraint(PathConstraint) - Method in class org.intermine.web.logic.query.DisplayConstraint

setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

Set the ObjectStore alias.

setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Set the ObjectStore alias.

setOsAlias(String) - Method in class org.intermine.task.StaticMethodTask

Set the os alias.

setOSAlias(String) - Method in class org.intermine.web.task.CreateSearchIndexTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.ProfileReadTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask

Set the alias of the main object store.

setOSAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask

Set the alias of the main object store.

setOsb(ObjectStoreBag) - Method in class org.intermine.api.profile.InterMineBag

Sets the ObjectStoreBag.

setOsName(String) - Method in class org.intermine.bio.task.OboConverterTask

Set the objectstore name

setOsName(String) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask

Set the ObjectStore for which to generate the data.

setOsName(String) - Method in class org.intermine.task.AnalyseDbTask

Set the database alias

setOsName(String) - Method in class org.intermine.task.BuildDbTask

Sets the objectstore

setOsName(String) - Method in class org.intermine.task.ConverterTask

Set the objectstore name

setOsName(String) - Method in class org.intermine.task.PostProcessorTask

Set the ObjectStore alias.

setOsName(String) - Method in class org.intermine.task.RetrieveMetadataTask

Sets the os alias

setOsName(String) - Method in class org.intermine.task.StoreMetadataTask

Sets the database alias

setOut(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask

Set the output handler.

setOuterInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

setOuterJoin(boolean) - Method in class org.intermine.pathquery.Node

Sets whether this should be an outer join.

setOuterJoins(PathQuery, String) - Method in class org.intermine.pathquery.PathQueryHandler

Given a path that may contain ':' characters to represent outer joins, find each : separated segment and set the status for that join to OUTER.

setOuterJoinStatus(String, OuterJoinStatus) - Method in class org.intermine.pathquery.PathQuery

Sets the outer join status of the last part of a given path in this query.

setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever

Set the output file name

setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever

Set the output file name

setOutputFile(File) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask

Sets the value of outputFile

setOutputFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask

Sets the value of outputFile.

setOutputFile(File) - Method in class org.intermine.bio.task.SOToModelTask

Set the output file to write generated additions XML to.

setOutputFile(File) - Method in class org.intermine.task.AcceptanceTestTask

Set the File to write output to

setOutputFile(File) - Method in class org.intermine.task.ModelMergerTask

Path of file to write resulting model to.

setOutputFile(File) - Method in class org.intermine.task.SummariseObjectStoreTask

Set the name of the file to write the summary into

setOverwriting(boolean) - Method in class org.intermine.web.struts.ImportTagsForm

Set the overwriting flag.

setOverwriting(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm

Set the overwriting flag.

setPackageName(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery

Set the package name NOTE: this method is merely here to make this a Bean.

setPage(Page) - Method in interface org.intermine.webservice.client.core.Request

Set the page for this request.

setPage(Page) - Method in class org.intermine.webservice.client.core.RequestImpl

Specify what section of the result set you wish to retrieve.

setPageAndPageSize(int, int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Set the page size and page together.

setPageName(String) - Method in class org.intermine.web.struts.ModifyBagForm

setPageName(String) - Method in class org.intermine.web.struts.ModifyTemplateForm

setPageSize(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Set the page size of the table

setPageSize(String) - Method in class org.intermine.web.struts.ChangeTableSizeForm

Set the page size

setPageSize(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag

setParameter(String, String) - Method in interface org.intermine.webservice.client.core.Request

Sets parameter

setParameter(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl

Sets parameter

setParameterName(String) - Method in class org.intermine.web.logic.template.ConstraintInput

setParameters(List<?>) - Method in class org.intermine.objectstore.query.iql.IqlQuery

Set the parameters

setParameters(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

A JSON string representing custom parameters for this displayer.

setParentTermId(String) - Method in class org.intermine.bio.ontology.OboRelation

setPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager

Change a user's password A check should be made prior to this call to ensure a Profile exists

setPassword(String) - Method in class org.intermine.web.struts.CreateAccountForm

setPassword(String) - Method in class org.intermine.web.struts.LoginForm

Sets the value of password

setPassword(String) - Method in class org.intermine.webservice.server.WebServiceInput

setPassword2(String) - Method in class org.intermine.web.struts.CreateAccountForm

setPath(String) - Method in class org.intermine.web.logic.config.InlineListConfig

Path set from WebConfig, ie "probeSets.primaryIdentifier"

setPath(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of path

setPathConstraints(String, List<? super PathConstraint>) - Static method in class org.intermine.web.logic.widget.config.WidgetConfig

Turn a string representing a set of constraints into a list of constraints.

setPathId(String) - Method in class org.intermine.web.logic.template.ConstraintInput

setPathQuery(PathQuery) - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

setPathsString(String) - Method in class org.intermine.web.struts.TableExportForm

Set the paths string

setPathStrings(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setPdbOrganisms(String) - Method in class org.intermine.bio.dataconversion.PdbConverter

Sets the list of taxonIds that should be imported if using split input files.

setPerm(String) - Method in class org.intermine.task.GrantTask

The permission to grant: SELECT, INSERT, UPDATE, DELETE, RULE, REFERENCES, TRIGGER, ALL

setPlacement(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set the data category name under which this displayer should appear.

setPlainTextContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets plain text content type.

setPlainTextHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for plain text output.

setPopulationBagName(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

Set the bag's name for reference population

setPreference(Profile, String, String) - Method in class org.intermine.api.profile.PreferencesManager

SetPreferencesService - Class in org.intermine.webservice.server.user

A service to set one or more preferences for a user.

SetPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.SetPreferencesService

setPrefix(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

Only used for MGI for now

setPrimaryIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setProcessors(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter

Set the class names of the ChadoProcessors to run.

setProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the user profile in the session.

setProfileId(Integer) - Method in class org.intermine.api.profile.InterMineBag

Sets the profileId - moves this bag from one profile to another.

setPropertiesOrigins(ServletContext, Map<String, List<String>>) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the origins of the web properties on the servlet context.

setPropertyName(String) - Method in class org.intermine.web.struts.EditPropertiesForm

Set the property name.

setPropertyValue(String) - Method in class org.intermine.web.struts.EditPropertiesForm

Set the value of the property

setProteinNames(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setPublication(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

setPublicId(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput

Sets id of object.

setPubmedOrganisms(String) - Method in class org.intermine.bio.dataconversion.PubMedGeneConverter

Sets the list of taxonIds that should be imported

setPubs(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setPValue(String) - Method in class org.intermine.web.struts.WidgetForm

setQuery(String) - Method in class org.intermine.task.RunIqlQueryTask

An query string to execute, may be IQL or SQL by format parameter must be set correctly, richard

setQuery(HttpSession, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods

Set the current query on the session.

setQuery(String) - Method in class org.intermine.web.struts.QueryForm

setQueryBuilder(String) - Method in class org.intermine.web.struts.ImportQueriesForm

Set the queryBuilder field.

setQueryClass(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

If the name of a class is set will only load objects of that type.

setQueryInfo(PathQuery, ResultsInfo) - Method in class org.intermine.api.query.WebResultsExecutor

Sets a ResultsInfo entry in the infoCache for a given PathQuery.

setQueryName(String) - Method in class org.intermine.web.struts.SaveQueryForm

Set the query name

setQueryString(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery

Set the query String NOTE: this method is merely here to make this a Bean.

setQueryXml(String) - Method in class org.intermine.webservice.client.services.QueryService.QueryRequest

Adds the query to be run.

setRangeConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the range constraint value.

setRangeLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Set the value of rangeLabel

setRangeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

setRedundant(boolean) - Method in class org.intermine.bio.ontology.OboRelation

setReference(String, String) - Method in class org.intermine.xml.full.Item

Add a reference to this item.

setReference(String, Item) - Method in class org.intermine.xml.full.Item

Add a reference that points to a particular item.

setRefId(String) - Method in class org.intermine.xml.full.Reference

Set the refId of this field

setRefIds(List<String>) - Method in class org.intermine.xml.full.ReferenceList

Set the references in this collection

setRelationship(OboTypeDefinition) - Method in class org.intermine.bio.ontology.OboRelation

setReplacesFields(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set the comma separated list of field names that should not be displayed on the report page when this displayer is used.

setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter

Sets header and content type of result in response.

setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter

Sets header and content type of result in response.

setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.TabHttpExporter

Sets header and content type of result in response.

setResultsTable(HttpSession, String, PagedTable) - Static method in class org.intermine.web.logic.session.SessionMethods

setRetryCount(int) - Method in class org.intermine.webservice.client.util.HttpConnection

Sets retry count.

setReturnToString(String) - Method in class org.intermine.web.struts.LoginForm

Sets the URL to return to if the login is successful.

setRowFormatter(RowFormatter) - Method in class org.intermine.webservice.server.output.FlatFileFormatter

Set the row formatter

setRows(int) - Method in class org.intermine.objectstore.query.ResultsInfo

Sets the estimated number of rows in the results.

setRows(List<List<String>>) - Method in class org.intermine.web.tags.table.TableTag

Set table rows.

setRowSpan(Integer) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Set how many rows this identifier spans

setSavedTemplateQuery(SavedTemplateQuery) - Method in class org.intermine.api.template.ApiTemplate

Sets the saved template query object.

setSavePopulation(boolean) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

setSchemafile(String) - Method in class org.intermine.task.BuildDbTask

Adds the schemafile to be processed.

setScope(String) - Method in class org.intermine.web.struts.TemplateForm

Set the template scope.

setScore(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setScore(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setSectionOnRight(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Set whether this field should be rendered in its own section on the right side of the page.

setSectionTitle(String) - Method in class org.intermine.web.logic.config.FieldConfig

Set the section title (if sectionOnRight == true).

setSelectable(boolean) - Method in class org.intermine.api.results.Column

Sets the value of selectable

setSelected(boolean) - Method in class org.intermine.web.logic.query.MetadataNode

Sets the value of selected

setSelected(String[]) - Method in class org.intermine.web.struts.ModifyTemplateForm

Sets the selected templates

setSelected(String[]) - Method in class org.intermine.web.struts.WidgetForm

setSelectedBagOp(ConstraintOp) - Method in class org.intermine.web.logic.query.DisplayConstraint

Set the seletedBagOp

setSelectedBags(String[]) - Method in class org.intermine.web.struts.ModifyBagForm

Sets the selected bags

setSelectedBagValue(String) - Method in class org.intermine.web.logic.query.DisplayConstraint

Set the seletedBagValue returned bye the getSelectedValue if the bag is selected

setSelectedClass(String) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

setSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

setSelectedElements(String[]) - Method in class org.intermine.web.struts.ModifyBagDetailsForm

Set the list of selectedElements

setSelectedExtraAttribute(String) - Method in class org.intermine.web.struts.WidgetForm

setSelectedObjects(String[]) - Method in class org.intermine.web.struts.BagUploadConfirmForm

Sets the ids of the selected objects - ie. those that should be included in the new bag

setSelectedObjects(String[]) - Method in class org.intermine.web.struts.SaveBagForm

Sets the selected objects

setSelectedQueries(String[]) - Method in class org.intermine.web.struts.ModifyQueryForm

Sets the selected queries

setSelectionIds(Map<Integer, String>) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

setSeqClsName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the sequenceClassName

setSeqDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the seqDataSourceName

setSeqHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the name of GFF3SeqHandler to use when processing.

setSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set sequence item created for this record, should not be edited in handler.

setSequence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setSequenceType(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask

Set the sequence type to be passed to the FASTA parser.

setSeriesLabels(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setSeriesPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setSeriesValues(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setServiceUrl(String) - Method in interface org.intermine.webservice.client.core.Request

Sets service URL.

setServiceUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl

Sets service URL.

setSession(HttpSession) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

setShowExtraConstraint(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint

setShowIdentifier(Boolean) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow

Set to show the identifier in this row

setShowImmediately(Boolean) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set if we should display the displayer immediately

setShowInHeader(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig

Show this list in the header?

setShowInInlineCollection(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Set the showInInlineCollection flag.

setShowInListAnalysisPreviewTable(Boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Specify if we want to show this field for an object in list analysis page table preview

setShowInQB(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Shall we show this field in a QueryBuilder?

setShowInResults(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Set the showInResults flag.

setShowInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig

Set the showInSummary flag.

setShowLinksToObjects(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig

Shall we show links to the objects's report pages?

setShowOnLeft(String) - Method in class org.intermine.web.logic.config.Displayer

setSingleton(boolean) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression

Sets whether the collection should be a singleton collection, or whether it should be a collection of ResultRows.

setSize(int) - Method in class org.intermine.webservice.server.lists.FlatListFormatter

setSize(int) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter

setSize(int) - Method in class org.intermine.webservice.server.lists.JSONListFormatter

setSize(int) - Method in interface org.intermine.webservice.server.lists.ListFormatter

set the size of the list.

setSoFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask

Sets the File containing the SO OBO data.

setSoFile(File) - Method in class org.intermine.bio.task.SOToModelTask

Sets the File containing the SO OBO data.

setSOTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook

For an item, set the SO term reference if one is not already set.

setSoTermListFile(File) - Method in class org.intermine.bio.task.SOToModelTask

Set the file containing a list of SO terms to be added to the data model.

setSource(Integer, String, Source) - Method in class org.intermine.dataloader.DataTracker

Set the Source for a field of an object in the database

setSource(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the ObjectStore that is the data source.

setSource(Source) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl

Sets the source of the data, so we know what the primary keys are, and can fetch that extra data.

setSourceName(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the source name, as used by primary key priority config.

setSourceName(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set the source name, as used by primary key priority config.

setSourceName(String) - Method in class org.intermine.task.DirectDataLoaderTask

Set the source name, as used by primary key priority config.

setSourceName(String) - Method in class org.intermine.task.FullXmlConverterTask

Set the source name, as used by primary key priority config.

setSourceType(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Set the source type, as used by primary key priority config.

setSourceType(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set the source type, as used by primary key priority config.

setSourceType(String) - Method in class org.intermine.task.DirectDataLoaderTask

Set the source type, as used by primary key priority config.

setSrc(String) - Method in class org.intermine.web.logic.config.Displayer

Set the source of this displayer

setStart(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Set start value

setStart(long) - Method in class org.intermine.objectstore.query.ResultsInfo

Sets the estimated amount of time taken to produce the first row of the results.

setStart(int) - Method in class org.intermine.webservice.client.core.RequestImpl

Set the start parameter.

setStart(Integer) - Method in class org.intermine.webservice.server.WebServiceInput

Sets from which index should be results returned 1-based.

setStartClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setStartClassDisplay(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

setStartingPoints(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the starting point class names as a space seperated list.

setState(BagState) - Method in class org.intermine.api.profile.InterMineBag

Set bag state

setState(String, String) - Static method in class org.intermine.dwr.AjaxServices

Set state that should be saved during the session.

setState(String, Object) - Method in class org.intermine.web.logic.results.WebState

Set attribute.

setStoreHook(DataConverterStoreHook) - Method in class org.intermine.dataconversion.DataConverter

Set a hook for this converter that will be called just before each Item is stored.

setStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

setStrand(String) - Method in class org.intermine.bio.io.bed.BEDRecord

setStrand(String) - Method in class org.intermine.bio.io.gaf.GAFRecord

setStrand(String) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

Set strand value

setStyle(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Sets element style.

setStyleClass(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag

Sets css style class of element.

setSubclass(String) - Method in class org.intermine.web.logic.querybuilder.SummaryPath

Sets the subclass on this path.

setSubclassValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Sets the value of subclassValue

setSubject(String) - Method in class org.intermine.web.struts.ContactForm

setSubject(String) - Method in class org.intermine.web.task.IssueTokenTask

Bean-style setter, as per the ant spec.

setSubTitle(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the subtitle.

setSubTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle

Set subtitle(s) path(s) for the object, e.g.: organism.shortName => D. melanogaster

setSubType(String) - Method in class org.intermine.webservice.client.core.ContentType

setSummarise(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set the summarise flag.

setSuperuser(boolean) - Method in class org.intermine.api.profile.Profile

Set the superuser flag and store it in userprofile database

setSuperuserPassword(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Set the superuser's initial password.

setSuperUsers(String[]) - Method in class org.intermine.web.struts.ModifySuperUserForm

Sets the super users

setSwitchable(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

setSwitchOff(String, String) - Method in class org.intermine.web.struts.TemplateForm

Set the SwitchOff ability.

setSwitchOffAbility(PathConstraint, SwitchOffAbility) - Method in class org.intermine.template.TemplateQuery

Sets the sbitch-off-ability of a constraint.

setSwitchOffAbility(SwitchOffAbility) - Method in class org.intermine.web.logic.query.DisplayConstraint

Set the switchOffAbility

setTabContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets tab separated values content type.

setTabHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for tab separated values output.

setTable(String) - Method in class org.intermine.web.struts.TableExportForm

Set the table identifier to look up in the servlet context

setTableDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type

Set the table displayer for this Type

setTableid(String) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

setTagValues(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboTerm

Sets the variable holding the raw tagValues that created this Term.

setTarget(String) - Method in class org.intermine.bio.task.GFF3ConverterTask

Set the target ObjectStore alias

setTaxonId(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

setTaxonId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry

setTempdir(File) - Method in class org.intermine.task.BuildDbTask

Sets the directory for temporary files including sql output

setTemplateButton(String) - Method in class org.intermine.web.struts.ModifyTemplateForm

setTemplateLabel(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

Set the template label.

setTemplateParameters(List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest

Set some template parameters.

setTemplatesummary(List<Object>) - Method in class org.intermine.web.logic.query.DisplayConstraint

setTemplatesXml(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Set the templates xml file.

setTermClass(String) - Method in class org.intermine.bio.task.OboConverterTask

Set the term class name

setText(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink

Set

setText(String) - Method in class org.intermine.web.struts.BuildBagForm

Set the query string

setTextToFind(String) - Method in class org.intermine.web.struts.FindInListForm

setTgtDir(File) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask

Set the target directory

setTgtLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set the tgtLocation item for this record.

setTgtOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Get the tgtOrganism item to use in this handler

setTgtSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler

Set tgtSequence item created for this record, should not be edited in handler.

setThickEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setThickEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setThickStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord

setThickStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord

setThreshold(int) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

This sets the threshold above which a temp table will be used for deletes.

setTileName(String) - Method in class org.intermine.web.logic.aspects.Aspect

Set the name of the tile/page to embed in the centre of the data set homepage.

setTimeLimit(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext

Sets the optimiser's maximum effort time, in milliseconds.

setTimeout(int) - Method in class org.intermine.webservice.client.util.HttpConnection

Sets timeout.

settings - Variable in class org.intermine.sql.Database

setTitle(String) - Method in class org.intermine.api.template.ApiTemplate

setTitle(String) - Method in class org.intermine.pathquery.PathQuery

Sets the name of the query.

setTitle(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setTitle(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm

setTitle(String) - Method in class org.intermine.web.struts.TemplateSettingsForm

Set the title

setToggledElements(Map<String, Boolean>) - Method in class org.intermine.web.logic.results.WebState

Sets map of ids and its state.

setToken(String) - Method in class org.intermine.web.struts.PasswordResetForm

Sets the value of token.

setToken(String) - Method in class org.intermine.web.task.VerifyTokenTask

Bean-style setter for token, as per ant spec.

setTrackQueue(Queue<Track>) - Method in class org.intermine.api.tracker.AbstractTracker

Set the queue of tracks

setTransitive(boolean) - Method in class org.intermine.bio.ontology.OboTypeDefinition

setTransitiveOver(List<String>) - Method in class org.intermine.bio.ontology.OboTypeDefinition

setTreatColNames(boolean) - Method in class org.intermine.web.tags.table.TableTag

setType(String) - Method in class org.intermine.api.beans.ObjectDetails

setType(String) - Method in class org.intermine.api.profile.InterMineBag

setType(String) - Method in class org.intermine.bio.io.gff3.GFF3Record

Set the type of this record.

setType(String) - Method in class org.intermine.pathquery.Node

Set the value of type

setType(String) - Method in class org.intermine.task.ModelOutputTask

Set the type of model output required.

setType(String) - Method in class org.intermine.web.logic.query.MetadataNode

Set the value of type

setType(String) - Method in class org.intermine.web.struts.BuildBagForm

Set the bag type

setType(String) - Method in class org.intermine.web.struts.TableExportForm

Set the type

setType(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag

Sets type of tag.

setType(String) - Method in class org.intermine.webservice.client.core.ContentType

Sets main content type.

setType(Request.RequestType) - Method in interface org.intermine.webservice.client.core.Request

setType(Request.RequestType) - Method in class org.intermine.webservice.client.core.RequestImpl

setType(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput

Sets object type.

setTypeClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setTypes(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig

Set the types this displayer should be used for as a comma separated list of unqualified class names.

setUniprot(String) - Method in class org.intermine.bio.util.OrganismData

setUniprotOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter

Sets the list of taxonIds that should be imported if using split input files.

setUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

setUp() - Method in class org.intermine.task.CreateIndexesTask

Sets up the instance variables

setupDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Sets up the database for storing precomputed tables

setupFieldValues() - Method in class org.intermine.web.logic.results.ReportObject

Setup fieldValues HashMap

setUpPermission(InterMineAPI, ProfileManager.ApiPermission) - Static method in class org.intermine.web.logic.profile.LoginHandler

Does whatever needs to be done to a permissions object to get it ready for a life cyle in a web service request.

setUpProfile(HttpSession, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler

Initialises a profile for the current user based on their user name and password.

setUpProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler

Sets up a profile ready for a session in InterMine.

setUrl(String) - Method in class org.intermine.bio.task.OboConverterTask

Set the url for the source of the ontology

setUrl(String) - Method in class org.intermine.web.logic.aspects.AspectSource

Set the URL to source website.

setUrl(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink

Set

setUrl(String) - Method in interface org.intermine.webservice.client.core.Request

Sets whole request URL.

setUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl

Sets whole request URL.

setUseBagConstraint(String, boolean) - Method in class org.intermine.web.struts.TemplateForm

Set value of useBagConstraint for given constraint key.

setUseJoin(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

setUser(String) - Method in class org.intermine.task.GrantTask

Set user to grant permissions to

setUserId(Integer) - Method in class org.intermine.api.profile.Profile

Set the userId

setUsername(String) - Method in class org.intermine.web.struts.CreateAccountForm

setUsername(String) - Method in class org.intermine.web.struts.LoginForm

Sets the value of username

setUsername(String) - Method in class org.intermine.web.struts.RequestPasswordForm

Sets the value of username

setUsername(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Set the account name to laod template to.

setUsername(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Set the account name to load template to.

setUsername(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set the account name to laod template to.

setUserName(String) - Method in class org.intermine.webservice.server.WebServiceInput

setUserProfileAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileReadTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackReadTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask

Set the alias of the userprofile database.

setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask

Set the alias of the userprofile object store.

setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateTrackTableTask

Set the alias of the userprofile object store.

setValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput

Sets constraint value.

setValue(B) - Method in class org.intermine.webservice.server.core.Pair

setValue(String) - Method in class org.intermine.xml.full.Attribute

Set the value of this field

setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Sets the verboseQueryLog configuration option.

setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Sets the verboseQueryLog configuration option.

setView(String) - Method in class org.intermine.web.struts.TemplateForm

Set the selected alternative view name.

setViews(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig

setVisible(boolean) - Method in class org.intermine.api.results.Column

Sets the value of visible

setWebConfig(ServletContext, WebConfig) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the WebConfig into the ServletContext.

setWebConfig(WebConfig) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig

setWebProperties(ServletContext, Properties) - Static method in class org.intermine.web.logic.session.SessionMethods

Sets the web properties in the session.

setWhichInput(String) - Method in class org.intermine.web.struts.BuildBagForm

Set the method the user used to upload her bag.

setWidgetid(String) - Method in class org.intermine.web.struts.WidgetForm

setWidgets(LinkedList) - Method in class org.intermine.web.logic.config.Type

setWidgetTitle(String) - Method in class org.intermine.web.struts.WidgetForm

used on results page for description: "results for widget XYZ"

setWriter(PrintWriter) - Method in class org.intermine.webservice.server.output.StreamedOutput

Sets associated writer

setXml(String) - Method in class org.intermine.web.struts.ImportTagsForm

Set the xml.

setXml(String) - Method in class org.intermine.web.struts.ImportXMLForm

Set the xml.

setXml(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput

Sets xml query string.

setXMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets XML content type.

setXMLFormat() - Method in class org.intermine.webservice.client.core.RequestImpl

Set the format as XML format.

setXMLHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil

Sets response header and content type for XML output.

setXmlResource(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask

Set XML resource name (to load data from classloader).

setXmlResource(String) - Method in class org.intermine.task.FullXmlConverterTask

Set XML resource name (to load data from classloader).

setXref(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config

shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager

Share the bag given in input with the user which userName input

shareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager

Let the recipient gain access to this bag in future uses of the application.

shareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager

Share the bag given in input with user which userName is given in input

shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.SharedBagManager

Share the bag given in input with user which userName is given in input To be used ONLY when deserialising the user-profile from XML.

SHARED_BAGS - Static variable in class org.intermine.api.bag.SharedBagManager

the table name

SharedBagBinding - Class in org.intermine.api.xml

Parse the shared bags in XML format

SharedBagBinding() - Constructor for class org.intermine.api.xml.SharedBagBinding

SharedBagHandler - Class in org.intermine.api.xml

Handle parsing of shared bags

SharedBagHandler(List<Map<String, String>>) - Constructor for class org.intermine.api.xml.SharedBagHandler

Constructor

SharedBagManager - Class in org.intermine.api.bag

Singleton manager class for shared bags.

SharingBagUsersController - Class in org.intermine.web.struts

Controller for the inline tag editing tile

SharingBagUsersController() - Constructor for class org.intermine.web.struts.SharingBagUsersController

SharingInvite - Class in org.intermine.api.bag

A representation of an invitation to share a resource.

SharingInvite(InterMineBag, String) - Constructor for class org.intermine.api.bag.SharingInvite

Constructor.

SharingInvite(InterMineBag, String, String) - Constructor for class org.intermine.api.bag.SharingInvite

Constructor.

SharingInvite(InterMineBag, String, String, Date, Date, Boolean) - Constructor for class org.intermine.api.bag.SharingInvite

Constructor.

SharingInvite.IntermediateRepresentation - Class in org.intermine.api.bag

A structure for holding data we read from the DB.

SharingInvite.IntermediateRepresentation() - Constructor for class org.intermine.api.bag.SharingInvite.IntermediateRepresentation

SharingInvite.NotFoundException - Exception in org.intermine.api.bag

Exception thrown when we can't find a shared invitation.

shortName - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder

shouldCancelQuery() - Method in interface org.intermine.web.logic.query.QueryMonitor

Called intermittently while a query is run providing an opportunity to cancel the query.

shouldCancelQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Return true if tickle has not been called in a period of time greater than the timeout value.

shouldSavePopulation() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

showColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Deprecated.

as we don't hide columns any more

shuffle(Map<String, V>, int) - Static method in class org.intermine.web.logic.WebUtil

takes a map and puts it in random order also shortens the list to be map.size() = max

shutdown() - Method in class org.intermine.api.tracker.TrackerDelegate

Called from ShutdownHook.

shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

Called by the ShutdownHook on shutdown.

shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Called by the StatsShutdownHook on shutdown

shutdown() - Method in class org.intermine.sql.Database

Logs stuff

shutdown() - Method in interface org.intermine.util.Shutdownable

Shuts down an instance.

shutdown() - Static method in class org.intermine.util.ShutdownHook

Performs the shutdown.

shutdown() - Method in class org.intermine.web.context.InterMineContext

Send the signal that shutdown is happening - try and release resources.

Shutdownable - Interface in org.intermine.util

An interface for any object that can be shut down by the ShutdownHook.

ShutdownHook - Class in org.intermine.util

This class provides a "shutdown" service to other classes.

SimpleConstraint - Class in org.intermine.objectstore.query

Represents a constraint between two QueryEvaluable types.

SimpleConstraint(QueryEvaluable, ConstraintOp, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.SimpleConstraint

Construct a Constraint.

SimpleConstraint(QueryEvaluable, ConstraintOp) - Constructor for class org.intermine.objectstore.query.SimpleConstraint

Construct a Constraint.

simpleConstraintToString(SqlGenerator.State, StringBuffer, SimpleConstraint, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a SimpleConstraint object into a String suitable for putting in an SQL query.

simpleCreateObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil

Create a new object given a class, which may be an interface.

SingleTemplateService - Class in org.intermine.webservice.server.template

Service that responds with a single template.

SingleTemplateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.SingleTemplateService

SINGLETON - Static variable in class org.intermine.util.NullFirstComparator

Publicly-accessible instance

SingletonResults - Class in org.intermine.objectstore.query

This class is equivalent to a Result object with ResultRows consisting only of single items

SingletonResults(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.SingletonResults

Constructor for a SingletonResults object

SingletonResults(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.SingletonResults

Constructor for a SingletonResults object, given a ResultsBatches object.

singletonResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

size() - Method in class org.intermine.api.profile.StorableBag

Returns the number of elements in the bag.

size() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl

size() - Method in class org.intermine.api.results.WebResults

size() - Method in class org.intermine.api.search.SearchResults

size() - Method in class org.intermine.objectstore.proxy.ProxyCollection

Gets the number of elements in this collection

size() - Method in class org.intermine.objectstore.query.Results

Gets the number of results rows in this Results object

size(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches

Gets the number of results rows in this Results object.

SIZE - Static variable in class org.intermine.objectstore.query.ResultsInfo

Denotes that the result of getRows() is the known size of the results.

size() - Method in class org.intermine.util.AlwaysMap

size() - Method in class org.intermine.util.ConsistentSet

Return the number of elements in this Set.

size() - Method in class org.intermine.util.IdentityMap

size() - Method in class org.intermine.util.IntPresentSet

Returns the number of ints present.

size() - Method in class org.intermine.util.IntToIntMap

Returns the number of mappings to non-minus-one ints present.

size() - Method in class org.intermine.util.PseudoSet

size() - Method in class org.intermine.util.ReferenceMap

size - Variable in class org.intermine.web.logic.results.InlineResultsTable

size() - Method in class org.intermine.webservice.client.lists.ItemList

Synonym for getSize()

size() - Method in class org.intermine.webservice.client.results.JsonRow

size() - Method in class org.intermine.webservice.client.results.ResultRowList

sizeOfArray(Object[]) - Static method in class org.intermine.sql.writebatch.TableBatch

Calculates the size of an array, in bytes.

sizeOfList(List<Object[]>) - Static method in class org.intermine.sql.writebatch.TableBatch

Calculates the size of a List of arrays, in bytes.

SKELETON - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

skeletons - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

SKIP_BUILDER_PARAMETER - Static variable in class org.intermine.web.struts.TemplateAction

Name of skipBuilder parameter

SOClassNameMapMakerTask - Class in org.intermine.bio.task

A Task that reads a SO OBO files and writes a file mapping SO term names to FlyMine class names.

SOClassNameMapMakerTask() - Constructor for class org.intermine.bio.task.SOClassNameMapMakerTask

Create a new SOClassNameMapMakerTask object.

SoftReferenceMap<K,V> - Class in org.intermine.util

This is a Map implementation designed specifically for people intending to create a cache.

SoftReferenceMap() - Constructor for class org.intermine.util.SoftReferenceMap

SortableMap<K extends java.lang.Comparable<K>,V extends java.lang.Comparable<V>> - Class in org.intermine.web.logic

SortableMap extends a LinkedHashMap with some useful sorting features.

SortableMap() - Constructor for class org.intermine.web.logic.SortableMap

Default constructor.

SortableMap(Map<K, V>) - Constructor for class org.intermine.web.logic.SortableMap

Create new SortableMap based on the given Map.

sortConstraints(List<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery

A method to sort constraints by a given lists, provided to allow TemplateQuery to set a specific sort order that will be preserved in a round-trip to XML.

sortKeys() - Method in class org.intermine.web.logic.SortableMap

Sort this map ascending on keys in natural order (default).

sortKeys(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap

Sort this map on keys.

sortMap(Map<String, BigDecimal>) - Static method in class org.intermine.web.logic.widget.ErrorCorrection

Sort the map by values.

sortValues() - Method in class org.intermine.web.logic.SortableMap

Sort this map ascending on values in natural order (default).

sortValues(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap

Sort this map on values.

SOToModelTask - Class in org.intermine.bio.task

A Task that reads a SO OBO files and writes so_additions.xml

SOToModelTask() - Constructor for class org.intermine.bio.task.SOToModelTask

source - Variable in class org.intermine.dataloader.BatchingFetcher

SOURCE - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

source - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

Source - Class in org.intermine.dataloader

Represents a data source, by name and skeleton status.

Source(String, String, boolean) - Constructor for class org.intermine.dataloader.Source

Create a new source object.

Source(String, String) - Constructor for class org.intermine.dataloader.Source

Create a new source object that isn't a skeleton.

Source(String, boolean) - Constructor for class org.intermine.dataloader.Source

Create a new source object with no type information.

Source(String) - Constructor for class org.intermine.dataloader.Source

Create a new source object with no type information that isn't a skeleton

sourceKeys - Static variable in class org.intermine.dataloader.DataLoaderHelper

sourceName - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

sourceName - Variable in class org.intermine.dataloader.XmlDataLoaderTask

sourceName - Variable in class org.intermine.task.DirectDataLoaderTask

sourceName - Variable in class org.intermine.task.FullXmlConverterTask

SourcePriorityComparator - Class in org.intermine.dataloader

Comparator, that compares two InterMineObjects, with reference to a particular FieldDescriptor for priority.

SourcePriorityComparator(DataTracker, Class<? extends InterMineObject>, String, Source, InterMineObject, IntPresentSet, IntegrationWriterAbstractImpl, Source, Source, PriorityConfig) - Constructor for class org.intermine.dataloader.SourcePriorityComparator

Constructs a new Comparator for comparing objects for priority for a given field.

sourceToString(Source) - Method in class org.intermine.dataloader.DataTracker

Converts a Source to a source name.

sourceType - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask

SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

SPACE_SPLITTER - Static variable in class org.intermine.pathquery.PathQuery

A Pattern that finds spaces in a String.

split(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression

Takes a List of collections of String variables and returns a List of the same length, containing sections of the LogicExpression with those variables in.

SPLITTER - Static variable in class org.intermine.objectstore.intermine.NotXmlParser

A Pattern that will find delimiters.

sqlCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

SqlGenerator - Class in org.intermine.objectstore.intermine

Code to generate an sql statement from a Query object.

SqlGenerator.State - Class in org.intermine.objectstore.intermine

Internal representation of the State of the query as it is built up.

SqlGenerator.State() - Constructor for class org.intermine.objectstore.intermine.SqlGenerator.State

Constructor

SQLOperation<T> - Class in org.intermine.objectstore.intermine

A functional interface (oh, please come Java 8 - you cannot come soon enough) to help manage out-of-control boilerplate-itis in SQL code.

SQLOperation() - Constructor for class org.intermine.objectstore.intermine.SQLOperation

SQLStringable - Interface in org.intermine.sql.query

An interface for all classes that implement the getSQLString method.

StandardHttpExporter - Class in org.intermine.web.logic.export.http

Abstract class implementing functionality common for exporters exporting table in simple format like comma separated format.

StandardHttpExporter() - Constructor for class org.intermine.web.logic.export.http.StandardHttpExporter

Constructor.

start - Variable in class org.intermine.dataconversion.FullXmlConverter

start - Variable in class org.intermine.objectstore.query.OverlapRange

start - Variable in class org.intermine.objectstore.query.ResultsInfo

start - Variable in class org.intermine.sql.precompute.BestQueryExplainer

start - Variable in class org.intermine.sql.query.ExplainResult

START_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser

Name of start parameter that determines index of first returned result.

START_PATHS - Static variable in class org.intermine.web.struts.InterMineRequestProcessor

Paths that can be used as initial pages ie. when there is no session.

startClass - Variable in class org.intermine.web.logic.widget.WidgetLdr

startContainsClass(String) - Method in class org.intermine.pathquery.Path

Return true if the first element in the path has the class given in input as type

startDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.BagQueryHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.InvitationHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.PreferencesHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.TagHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.InterMineBagHandler

InvalidBag

startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SavedQueryHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SharedBagHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.pathquery.PathQueryHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.template.xml.TemplateQueryHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.webservice.server.ServiceListingHandler

startElement(String, String, String, Attributes) - Method in class org.intermine.xml.full.FullHandler

startListening() - Method in class org.intermine.api.search.SearchRepository

Begin listening for events on the items of interest.

startPagedTableCount(PageTableQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods

Start a query running in the background that will return the row count of the collection.

startQuery(QueryMonitor, HttpSession, MessageResources, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods

Start the current query running in the background, then return.

startQueryCount(QueryCountQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods

Start a query running in the background that will return the row count of the query argument.

startQueryWithTimeout(HttpServletRequest, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods

Start the given query running in the background, then return, with a default timeout.

startTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Put query builder in template building mode.

StaticMethodTask - Class in org.intermine.task

Given a class name and method name, just invokes a static method.

StaticMethodTask() - Constructor for class org.intermine.task.StaticMethodTask

stats - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

statsBagTableTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

statsConTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

statsEstTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

statsExeTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

statsGenTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

statsOptTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

StatusDictionary - Class in org.intermine.webservice.server

HTTP status code dictionary.

STDDEV - Static variable in class org.intermine.objectstore.query.QueryFunction

Sample standard deviation of a number of rows

STDDEV - Static variable in class org.intermine.sql.query.Function

STDDEV operator - takes one operand

stm - Variable in class org.intermine.api.tracker.xml.TrackHandler

StockProcessor - Class in org.intermine.bio.dataconversion

A ChadoProcessor for the chado stock module.

StockProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.StockProcessor

Create a new ChadoProcessor

stop() - Method in class org.intermine.webservice.server.idresolution.JobJanitor

Let others tell us to stop.

stopListening() - Method in class org.intermine.api.search.SearchRepository

Stop listening for events

stopTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange

Bring the query builder out of template building mode and discard any unfinished template building.

StorableBag - Class in org.intermine.api.profile

Base class for representations of user's collections of objects stored in a database.

StorableBag() - Constructor for class org.intermine.api.profile.StorableBag

store(Connection) - Method in interface org.intermine.api.tracker.track.Track

Save into the table the track object representing the user activity

store(Connection) - Method in class org.intermine.api.tracker.track.TrackAbstract

store(Item, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor

Store the feature Item.

store(Item, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor

Store the feature Item.

store(Item, int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor

Store the feature Item.

store(Item) - Method in class org.intermine.dataconversion.DataConverter

Store a single XML Item

store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.DataConverter

Store a single XML ReferenceList

store(Attribute, Integer) - Method in class org.intermine.dataconversion.DataConverter

Store a single XML Attribute

store(Reference, Integer) - Method in class org.intermine.dataconversion.DataConverter

Store a single XML Reference

store(Collection<Item>) - Method in class org.intermine.dataconversion.DataConverter

Store a Collection of XMl Items

store(Item) - Method in interface org.intermine.dataconversion.ItemWriter

Stores the given Item and all its associated attributes, references, and referencelists.

store(ReferenceList, Integer) - Method in interface org.intermine.dataconversion.ItemWriter

Stores the given ReferenceList after setting its item id.

store(Reference, Integer) - Method in interface org.intermine.dataconversion.ItemWriter

Stores the given Reference after setting its item id.

store(Attribute, Integer) - Method in interface org.intermine.dataconversion.ItemWriter

Stores the given Attribute after setting its item id.

store(Item) - Method in class org.intermine.dataconversion.MockItemWriter

Stores the given Item and all its associated attributes, references, and referencelists.

store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.MockItemWriter

Stores the given ReferenceList after setting its item id.

store(Reference, Integer) - Method in class org.intermine.dataconversion.MockItemWriter

Stores the given Reference after setting its item id.

store(Attribute, Integer) - Method in class org.intermine.dataconversion.MockItemWriter

Stores the given Attribute after setting its item id.

store(Item) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Stores the given Item and all its associated attributes, references, and referencelists.

store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Stores the given ReferenceList after setting its item id.

store(Reference, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Stores the given Reference after setting its item id.

store(Attribute, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Stores the given Attribute after setting its item id.

store(FastPathObject) - Method in class org.intermine.dataloader.DirectDataLoader

Store an object using the IntegrationWriter, buffering writes so that integration queries and database writes can be run in batches.

store(FastPathObject, Source, Source) - Method in interface org.intermine.dataloader.IntegrationWriter

Stores the given object in the objectstore.

store(FastPathObject, Source, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Stores the given object in the objectstore.

store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Stores the given object in the objectstore.

store(Object) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl

Store an object in this ObjectStore, delegates to internal ObjectStoreWriter.

store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

Stores the given object in the objectstore.

store(Database, String, String) - Static method in class org.intermine.modelproduction.MetadataManager

Store a (key, value) pair in the metadata table of the database

store(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Store an object in this ObjectStore.

store(Object) - Method in interface org.intermine.objectstore.ObjectStoreWriter

Store an object in this ObjectStore.

storeAll() - Method in class org.intermine.bio.dataconversion.GFF3Converter

store all the items

storeAll(Collection<Item>) - Method in interface org.intermine.dataconversion.ItemWriter

Stores the given Collection of Items and all their associated attributes, references, and referencelists.

storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.MockItemWriter

Stores the given Collection of Items and all their associated attributes, references, and referencelists.

storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter

Stores the given Collection of Items and all their associated attributes, references, and referencelists.

storeBinary(Database, String, byte[]) - Static method in class org.intermine.modelproduction.MetadataManager

Store a binary (key, value) pair in the metadata table of the database

storeException(HttpServletRequest, String, ActionMessage, ActionForward, String) - Method in class org.intermine.web.struts.InterMineExceptionHandler

Default implementation for handling an ActionMessage generated from an Exception during Action delegation.

storeInvites(Profile) - Method in class org.intermine.api.bag.InvitationHandler

storeItems() - Method in class org.intermine.bio.dataconversion.OboConverter

Convert DagTerms into Items and relation Items, and write them to the ItemWriter

storeLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager

Returns an OutputStream object with which to write a large binary value to the database.

StoreMetadataTask - Class in org.intermine.task

Store model metadata to a database

StoreMetadataTask() - Constructor for class org.intermine.task.StoreMetadataTask

storeSavedBag() - Method in class org.intermine.api.profile.StorableBag

Perform the actual insertion of data into the userprofile database.

storeTrack(Track) - Method in class org.intermine.api.tracker.AbstractTracker

Save into the table the track object representing the user activity

storeTrack(Track) - Method in interface org.intermine.api.tracker.Tracker

Save into the table a Track

storeWithConnection(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Performs store with a given Connection.

StreamedOutput - Class in org.intermine.webservice.server.output

Immediately as the data or error messages are added they are streamed via http connection.

StreamedOutput(PrintWriter, Formatter) - Constructor for class org.intermine.webservice.server.output.StreamedOutput

Constructor.

StreamedOutput(PrintWriter, Formatter, String) - Constructor for class org.intermine.webservice.server.output.StreamedOutput

Constructor.

STRING_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint

StringHelper - Class in org.intermine.api.query.range

StringHelper() - Constructor for class org.intermine.api.query.range.StringHelper

StringTableExporter - Class in org.intermine.web.logic.export.string

Simple exporter exporting table of strings.

StringTableExporter(PrintWriter, RowFormatter) - Constructor for class org.intermine.web.logic.export.string.StringTableExporter

Constructor.

stringToSource(String) - Method in class org.intermine.dataloader.DataTracker

Converts a string sourcename to a Source.

stringToSource(String, String) - Method in class org.intermine.dataloader.DataTracker

Converts a string sourcename to a Source if the type is known.

stripStart(String, Properties) - Static method in class org.intermine.util.PropertiesUtil

Strips the given string off the keys of the given Properties, and returns a new set of properties.

STRPOS - Static variable in class org.intermine.sql.query.Function

STRPOS operator - takes two operands.

SUB - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle

A subtitle.

SUBCLASSES - Static variable in class org.intermine.web.logic.Constants

ServletContext attribute, Map from unqualified type name to list of subclass names.

subclassValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

subIter - Variable in class org.intermine.api.results.ExportResultsIterator

subList(int, int) - Method in class org.intermine.objectstore.query.Results

subList(int, int) - Method in class org.intermine.webservice.client.results.ResultRowList

subMap - Variable in class org.intermine.util.ReferenceMap

SubMenuController - Class in org.intermine.web.struts

Controller for the submenu at the top of every page

SubMenuController() - Constructor for class org.intermine.web.struts.SubMenuController

submit(BagQueryRunner, JobInput) - Method in class org.intermine.api.idresolution.IDResolver

submit(BagQueryUpgrade) - Method in class org.intermine.api.idresolution.IDResolver

subquery - Variable in class org.intermine.objectstore.query.SubqueryConstraint

subquery - Variable in class org.intermine.objectstore.query.SubqueryExistsConstraint

SubQuery - Class in org.intermine.sql.query

A representation of a subquery that can be present in the FROM section of an SQL query.

SubQuery(Query, String) - Constructor for class org.intermine.sql.query.SubQuery

Constructor for this SubQuery object.

SubqueryConstraint - Class in org.intermine.objectstore.query

Constrain a QueryClass or QueryEvaluable to be within the select list of a given subquery.

SubqueryConstraint(QueryEvaluable, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint

Construct a SubqueryConstraint with a QueryEvaluable

SubqueryConstraint(QueryClass, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint

Construct a SubqueryConstraint with a QueryClass

SubQueryConstraint - Class in org.intermine.sql.query

A representation of a constraint where an AbstractValue is IN the results of a Query.

SubQueryConstraint(AbstractValue, Query) - Constructor for class org.intermine.sql.query.SubQueryConstraint

Constructor for SubQueryConstraint object.

subqueryConstraintToString(SqlGenerator.State, StringBuffer, SubqueryConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a SubqueryConstraint object into a String suitable for putting in an SQL query.

SubqueryExistsConstraint - Class in org.intermine.objectstore.query

Check if there are any rows in the subquery

SubqueryExistsConstraint(ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryExistsConstraint

Construct a SubqueryExistsConstraint

subqueryExistsConstraintToString(SqlGenerator.State, StringBuffer, SubqueryExistsConstraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Converts a SubqueryExistsConstraint object into a String suitable for putting in an SQL query.

subscribe(String, Properties) - Static method in class org.intermine.util.MailUtils

Subscribe the given email address to the mailing list specified in the mine config file

subscribeToList(String) - Method in class org.intermine.util.Emailer

Subscribe a user to a mailing list.

subscribeToList(String) - Method in class org.intermine.web.context.NullMailer

subSequence(int, int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).

subSequence - Variable in class org.intermine.objectstore.query.ClobAccess

subSequence(int, int) - Method in class org.intermine.objectstore.query.ClobAccess

Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).

subSequence(int, int) - Method in class org.intermine.objectstore.query.PendingClob

Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).

SUBSTR - Static variable in class org.intermine.sql.query.Function

SUBSTR operator - takes two or three operands.

SUBSTRING - Static variable in class org.intermine.objectstore.query.QueryExpression

Substring of specified length from index in string

SubTable - Class in org.intermine.webservice.server.core

A class that represents a table nested within a cell in another table.

SubTable(Path, List<Path>, List<List<Either<ResultCell, SubTable>>>) - Constructor for class org.intermine.webservice.server.core.SubTable

Construct a sub table.

subtabs - Variable in class org.intermine.web.logic.results.WebState

SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations

Constant representing logical substraction.

subtract(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations

Create a bag that contains the union of the bags provided minus the intersection of those bags.

SUBTRACT - Static variable in class org.intermine.objectstore.query.QueryExpression

Subtraction of two numeric fields

subtract(ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList

Remove the items in the given lists from this list.

subtract(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList

Remove the items in the given lists from this list.

subtract(Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList

Remove the items in the given lists from this list.

subtract(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList

Remove the items in the given lists from this list.

subtract(ListService.ListOperationInfo, ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

subtract(ListService.ListOperationInfo, ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

subtract(ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

subtract(ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

subtract(Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

subtract(ListService.ListOperationInfo, Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService

Subtract some lists from some other lists to produce a new list.

SUBTRACT_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput

Things to subtract

SUM - Static variable in class org.intermine.objectstore.query.QueryFunction

Sum of a number of rows

SUM - Static variable in class org.intermine.sql.query.Function

SUM(v) aggregate function - takes one operand.

summarise(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser

Populates the possibleValues data for a given TemplateQuery from the os.

summarise(String) - Method in class org.intermine.dwr.AjaxServices

Summarises the given template query.

summariseAsOccurrences(String) - Static method in class org.intermine.api.query.MainHelper.SummaryConfig

Returns whether the given field name is configured to be summarised as a count of occurrences.

SummariseObjectStoreTask - Class in org.intermine.task

Summarise an ObjectStore into a particular properties file.

SummariseObjectStoreTask() - Constructor for class org.intermine.task.SummariseObjectStoreTask

summariseQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor

Returns the results for a summary for a column in a PathQuery.

summariseQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor

summariseQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor

Summarise a query.

SummariseTemplatesAction - Class in org.intermine.web.struts

Action to summarise all templates.

SummariseTemplatesAction() - Constructor for class org.intermine.web.struts.SummariseTemplatesAction

summaryBatchSize - Variable in class org.intermine.api.query.QueryExecutor

summaryCallCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

SummaryConstraint - Class in org.intermine.web.logic.querybuilder

Representation of a PathQuery constraint with additional information for display in the QueryBuilder summary section.

SummaryConstraint(PathConstraint, String, boolean, String, String) - Constructor for class org.intermine.web.logic.querybuilder.SummaryConstraint

Construct with the underlying PathConstraint and additional details from the PathQuery.

summaryCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

SummaryPath - Class in org.intermine.web.logic.querybuilder

Representation of a query path with additional information for display in the QueryBulder summary section.

SummaryPath(Path, boolean, boolean) - Constructor for class org.intermine.web.logic.querybuilder.SummaryPath

Construct a summary path with details of whether the path is locked and/or forced to be an inner join.

SummaryService - Class in org.intermine.webservice.server

Serve up the paths used to summarise each class.

SummaryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SummaryService

Constructor

SummaryServlet - Class in org.intermine.webservice.server

Returns a summary field information.

SummaryServlet() - Constructor for class org.intermine.webservice.server.SummaryServlet

summaryTimes - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher

superUsers - Variable in class org.intermine.web.struts.ModifySuperUserForm

swapColumns(int, int) - Method in class org.intermine.web.logic.results.PagedTable

Deprecated.

Swap 2 columns

swapColumns(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction

Deprecated.

as we don't move columns any more

switchable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

SwitchOffAbility - Enum in org.intermine.template

Enumeration for describing the configuration on constraints on a TemplateQuery that determines whether a user is allowed to switch off a constraint, and if so what state it is in.

SymmetricDifference - Class in org.intermine.api.bag.operations

SymmetricDifference(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.SymmetricDifference

SynchronisedIterator<E> - Class in org.intermine.util

An Iterator that passes through to an underlying Iterator, synchronising all calls.

SynchronisedIterator(Iterator<E>) - Constructor for class org.intermine.util.SynchronisedIterator

Constructs a SynchronisedIterator from an Iterator.

synchroniseWithDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager

Synchronise with the underlying database

synonyms - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

synonyms - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

synToItem - Variable in class org.intermine.bio.dataconversion.OboConverter

T

TabFormatter - Class in org.intermine.webservice.server.output

Formats data to tab separated data format.

TabFormatter() - Constructor for class org.intermine.webservice.server.output.TabFormatter

Constructor.

TabFormatter(boolean) - Constructor for class org.intermine.webservice.server.output.TabFormatter

Construct, specifying whether or not to quote.

TabHttpExporter - Class in org.intermine.web.logic.export.http

Exporter that exports table with results in tab format.

TabHttpExporter() - Constructor for class org.intermine.web.logic.export.http.TabHttpExporter

Constructor.

table - Variable in class org.intermine.sql.logging.DatabaseWriter

table - Variable in class org.intermine.sql.query.Field

Table - Class in org.intermine.sql.query

A representation of a table that can be present in the FROM section of an SQL query.

Table(String, String) - Constructor for class org.intermine.sql.query.Table

Constructor for this Table object.

Table(String) - Constructor for class org.intermine.sql.query.Table

Constructor for this Table object, without an alias.

Table - Interface in org.intermine.sql.writebatch

An interface representing all changes to be made to an SQL table of some sort.

TABLE_INDEX - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager

TABLE_MAP - Static variable in class org.intermine.web.logic.Constants

Session attribute that holds cache of table identifiers to PagedTable objects.

TABLE_NAME - Static variable in class org.intermine.api.bag.SharingInvite

The DB table that holds the invitations

TableBatch - Class in org.intermine.sql.writebatch

A class representing all changes to be made to an SQL table.

TableBatch() - Constructor for class org.intermine.sql.writebatch.TableBatch

Constructor for this class.

TableCell - Class in org.intermine.webservice.server.core

A representation of a table cell.

TableCell(FastPathObject, Path, boolean) - Constructor for class org.intermine.webservice.server.core.TableCell

Construct a table cell.

TableCell(Path) - Constructor for class org.intermine.webservice.server.core.TableCell

Construct a table cell for a null value.

TableCellFormatter - Class in org.intermine.webservice.server.output

A formatter that will render a table cell.

TableCellFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.TableCellFormatter

TableController - Class in org.intermine.web.struts

Implementation of TilesAction.

TableController() - Constructor for class org.intermine.web.struts.TableController

tableCount - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

tableExists(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil

Tests if a table exists in the database

TableExportAction - Class in org.intermine.web.struts

Implementation of Action that allows the user to export a PagedTable to a file.

TableExportAction() - Constructor for class org.intermine.web.struts.TableExportAction

TableExportConfig - Class in org.intermine.web.logic.config

Configuration information for exporting.

TableExportConfig() - Constructor for class org.intermine.web.logic.config.TableExportConfig

TableExporterFactory - Class in org.intermine.web.logic.export.http

Factory class that creates and registers TableHttpExporter classes.

TableExporterFactory(WebConfig) - Constructor for class org.intermine.web.logic.export.http.TableExporterFactory

Constructor.

TableExportForm - Class in org.intermine.web.struts

Form to hold options for exporting.

TableExportForm() - Constructor for class org.intermine.web.struts.TableExportForm

Constructor

TableHttpExporter - Interface in org.intermine.web.logic.export.http

Implemented by objects that can export PagedTable.

TableJSONProcessor - Class in org.intermine.webservice.server.widget

Class to process the result returned by a table widgets in JSON format

TableJSONProcessor() - Constructor for class org.intermine.webservice.server.widget.TableJSONProcessor

tableNameForId(Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Returns the table name used by the ID fetch query.

tablenamesCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator

TableRowIterator - Class in org.intermine.webservice.server.core

A class for iterating over rows of results returned from the object store in a way that is very similar in shape to the raw results, but more tractable and more easily serialised and handled in other places.

TableRowIterator(PathQuery, Query, Results, Map<String, QuerySelectable>, Page, InterMineAPI) - Constructor for class org.intermine.webservice.server.core.TableRowIterator

Constructor.

TableRowService - Class in org.intermine.webservice.server.query.result

A service that produces results in nested rows for use in tables.

TableRowService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.TableRowService

tablesAltered - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

TableTag - Class in org.intermine.web.tags.table

Class rendering html table.

TableTag() - Constructor for class org.intermine.web.tags.table.TableTag

tableToCollections - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

tableToColNameArray - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

tableToInfo - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

TableWidget - Class in org.intermine.web.logic.widget

A table widget gets the values for a given path for all the items in a list.

TableWidget(TableWidgetConfig, InterMineBag, ObjectStore) - Constructor for class org.intermine.web.logic.widget.TableWidget

TableWidgetConfig - Class in org.intermine.web.logic.widget.config

TableWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.TableWidgetConfig

TableWidgetLdr - Class in org.intermine.web.logic.widget

TableWidgetLdr(WidgetConfig, InterMineBag, ObjectStore) - Constructor for class org.intermine.web.logic.widget.TableWidgetLdr

This class loads and formats the data for the count table widgets in the bag details page

TableWidgetService - Class in org.intermine.webservice.server.widget

Web service that returns a table widget for a given list.

TableWidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.TableWidgetService

Construct a TableWidgetService

TableWidgetsServlet - Class in org.intermine.webservice.server.widget

Servlet running WidgetsService.

TableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.TableWidgetsServlet

TableXMLProcessor - Class in org.intermine.webservice.server.widget

Class to process the result returned by a table widgets into a XML format

TabRowFormatter - Class in org.intermine.web.logic.export.rowformatters

Row formatter formats line as tab separated strings.

TabRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.TabRowFormatter

Constructor.

TabTableResult - Class in org.intermine.webservice.client.results

A utility class for parsing tab separated values in the results.

TabTableResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.TabTableResult

Constructor.

TabTableResult(String) - Constructor for class org.intermine.webservice.client.results.TabTableResult

Constructor.

TagBinding - Class in org.intermine.api.xml

Convert Tags from the Profile to and from XML

TagBinding() - Constructor for class org.intermine.api.xml.TagBinding

TagChecker - Interface in org.intermine.api.profile

An interface for checking the validity of tags.

TagFilter - Class in org.intermine.api.search

Class for filtering web-searchables based on their tags.

TagFilter(Collection<String>, Profile, String) - Constructor for class org.intermine.api.search.TagFilter

Constructor

Taggable - Interface in org.intermine.api.profile

An interface for items that may have tags stored for them in the user profile database.

TaggingEvent - Class in org.intermine.api.search

A representation of a notification that a tag has been changed on a web-searchable item.

TaggingEvent(WebSearchable, String, TaggingEvent.TagChange) - Constructor for class org.intermine.api.search.TaggingEvent

Constructor.

TaggingEvent.TagChange - Enum in org.intermine.api.search

The possible actions that this event can represent.

TagHandler - Class in org.intermine.api.profile

Extension of PathQueryHandler to handle parsing TemplateQueries

TagHandler(String, Set) - Constructor for class org.intermine.api.profile.TagHandler

Constructor

TagHandler(ProfileManager, String) - Constructor for class org.intermine.api.profile.TagHandler

Constructor

TagManager - Class in org.intermine.api.profile

Manager class for tags.

TagManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManager

Constructor.

tagManager - Variable in class org.intermine.api.search.SearchRepository

TagManager.TagException - Exception in org.intermine.api.profile

Class for reporting exceptions from tag manipulation actions.

TagManager.TagException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagException

Constructor.

TagManager.TagNameException - Exception in org.intermine.api.profile

Class for representing errors due to the use of illegal tag names.

TagManager.TagNameException() - Constructor for exception org.intermine.api.profile.TagManager.TagNameException

Constructor.

TagManager.TagNamePermissionException - Exception in org.intermine.api.profile

Class for representing errors due to the restricted nature of some tags.

TagManager.TagNamePermissionException() - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException

Constructor.

TagManager.TagNamePermissionException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException

Constructor.

TagManagerFactory - Class in org.intermine.api.profile

Factory class for creating TagManager objects.

TagManagerFactory(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManagerFactory

Constructor.

TagManagerFactory(ProfileManager) - Constructor for class org.intermine.api.profile.TagManagerFactory

Constructor.

TagMapper - Class in org.intermine.api.profile

A class that handles transforming a list of tags into a list of strings of different types.

TagMapper.Field - Enum in org.intermine.api.profile

The valid fields that can be read from a tag

tagName - Variable in class org.intermine.api.search.TaggingEvent

TagNames - Class in org.intermine.api.tag

TAGS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

Tags to apply

TagTypes - Class in org.intermine.api.tag

Known tag types.

targetAlias - Variable in class org.intermine.bio.task.GFF3ConverterTask

taxon - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

TEMP_SUFFIX - Static variable in class org.intermine.webservice.server.lists.ListInput

A suffix to attach to temporary lists

tempDir - Variable in class org.intermine.task.BuildDbTask

TEMPLATE - Static variable in class org.intermine.api.tag.TagTypes

Template.

TEMPLATE_ACTION_PATH - Static variable in class org.intermine.web.struts.TemplateAction

path of TemplateAction action

TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

TEMPLATE_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of class that tracks templates

TEMPLATE_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil

name of table that tracks templates

TemplateAction - Class in org.intermine.web.struts

Action to handle submit from the template page.

TemplateAction() - Constructor for class org.intermine.web.struts.TemplateAction

templateButton - Variable in class org.intermine.web.struts.ModifyTemplateForm

TemplateComparator - Class in org.intermine.template

Comparator used for ordering templates by title

TemplateComparator() - Constructor for class org.intermine.template.TemplateComparator

TemplateController - Class in org.intermine.web.struts

Controller for the template tile.

TemplateController() - Constructor for class org.intermine.web.struts.TemplateController

templateExecutions - Variable in class org.intermine.api.tracker.TemplatesExecutionMap

TemplateForm - Class in org.intermine.web.struts

Form to handle input from the template page

TemplateForm() - Constructor for class org.intermine.web.struts.TemplateForm

Constructor

templateFormToTemplateValues(TemplateForm, TemplateQuery) - Method in class org.intermine.web.struts.TemplateAction

The method returns a map of TemplateValue for each editable constraint.

TemplateHelper - Class in org.intermine.api.template

Static helper routines related to templates.

templateIsPublic(TemplateQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction

Utility function to determine whether the template is publicly accessible.

templateLabel - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

TemplateListAppendService - Class in org.intermine.webservice.server.template

A class to append items from a set of template results to a list.

TemplateListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateListAppendService

Constructor.

TemplateListAppendServlet - Class in org.intermine.webservice.server.template

Runs the query-to-list service to run queries and save them as lists.

TemplateListAppendServlet() - Constructor for class org.intermine.webservice.server.template.TemplateListAppendServlet

TemplateListController - Class in org.intermine.web.struts

Controller for the template list tile.

TemplateListController() - Constructor for class org.intermine.web.struts.TemplateListController

templateManager - Variable in class org.intermine.api.InterMineAPI

TemplateManager - Class in org.intermine.api.template

A TemplateManager provides access to all global and/or user templates and methods to fetch them by type, etc.

TemplateManager(Profile, Model) - Constructor for class org.intermine.api.template.TemplateManager

The TemplateManager references the super user profile to fetch global templates.

TemplateManager(Profile, Model, TemplateTracker) - Constructor for class org.intermine.api.template.TemplateManager

The TemplateManager references the super user profile to fetch global templates.

templateMapToXml(Map<String, TemplateQuery>, int) - Static method in class org.intermine.api.template.TemplateHelper

Given a Map of TemplateQueries (mapping from template name to TemplateQuery) return a string containing each template seriaised as XML.

TemplateParameter - Class in org.intermine.webservice.client.template

A simple class representing the group of parameters that define a template constraint A template parameter is a predefined constraint where you can specify the constraint operation and the constrained value.

TemplateParameter(String, String, String, String, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter

Create a new TemplateParameter for a simple value constraint.

TemplateParameter(String, String, Collection<String>, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter

Create a new TemplateParameter for a multi-value constraint.

TemplateParameter(String, String, String, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter

Create a new TemplateParameter for a unary constraint (such as IS NULL).

TemplatePopulator - Class in org.intermine.api.template

Configures original template.

TemplatePopulatorException - Exception in org.intermine.template

Exception thrown when errors occur populating a template query with values.

TemplatePopulatorException(String) - Constructor for exception org.intermine.template.TemplatePopulatorException

Constructs an TemplatePopulatorException with the specified detail message.

TemplatePopulatorException(Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException

Constructs an TemplatePopulatorException with the specified nested throwable.

TemplatePopulatorException(String, Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException

Constructs an TemplatePopulatorException with the specified detail message and nested throwable.

TemplatePrecomputeHelper - Class in org.intermine.api.template

Helper class providing methods for precomputing and summarising TemplateQuery objects.

TemplateProblemsController - Class in org.intermine.web.struts

Called before templateProblems.jsp

TemplateProblemsController() - Constructor for class org.intermine.web.struts.TemplateProblemsController

TemplateQuery - Class in org.intermine.template

A template query, which consists of a PathQuery, description, category, short name.

TemplateQuery(String, String, String, PathQuery) - Constructor for class org.intermine.template.TemplateQuery

Construct a new instance of TemplateQuery.

TemplateQuery(TemplateQuery) - Constructor for class org.intermine.template.TemplateQuery

Copy constructor.

TemplateQueryBinding - Class in org.intermine.template.xml

Convert PathQueries to and from XML

TemplateQueryBinding() - Constructor for class org.intermine.template.xml.TemplateQueryBinding

TemplateQueryHandler - Class in org.intermine.template.xml

Extension of PathQueryHandler to handle parsing TemplateQueries

TemplateQueryHandler(Map<String, TemplateQuery>, int) - Constructor for class org.intermine.template.xml.TemplateQueryHandler

Constructor

TemplateQueryUpdate - Class in org.intermine.api.profile

A class to update template queries to match a new Data model.

TemplateQueryUpdate(ApiTemplate, Model) - Constructor for class org.intermine.api.profile.TemplateQueryUpdate

Constructor.

TemplateRemovalService - Class in org.intermine.webservice.server.template

A service that deletes templates.

TemplateRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateRemovalService

TemplateResultInput - Class in org.intermine.web.logic.template

TemplateResultInput is parameter object representing parameters for TemplateResultService web service.

TemplateResultInput() - Constructor for class org.intermine.web.logic.template.TemplateResultInput

TemplateResultLinkGenerator - Class in org.intermine.webservice.server.template.result

Class that implements generating links of TemplateResultService web service.

TemplateResultLinkGenerator() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator

TemplateResultRequestParser - Class in org.intermine.webservice.server.template.result

Processes service request.

TemplateResultRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultRequestParser

TemplateResultRequestProcessor constructor.

TemplateResultService - Class in org.intermine.webservice.server.template.result

Web service that returns results of public template constrained with values in request.

TemplateResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultService

Construct with an InterMineAPI.

TemplateResultServlet - Class in org.intermine.webservice.server.template.result

Runs TemplateResultService web service.

TemplateResultServlet() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultServlet

Templates - Class in org.intermine.web.logic.template

A utility class with static methods for dealing with templates.

Templates.TemplateValueParseException - Exception in org.intermine.web.logic.template

An exception that we throw when we can't parse a template.

Templates.TemplateValueParseException(String) - Constructor for exception org.intermine.web.logic.template.Templates.TemplateValueParseException

Construct an exception with a message

TEMPLATES_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService

The key for the templates parameter

TemplatesController - Class in org.intermine.web.struts

Tiles controller for templates tile (page).

TemplatesController() - Constructor for class org.intermine.web.struts.TemplatesController

TemplateService - Class in org.intermine.webservice.client.services

The TemplateService represents the connection to the resource that returns results of templates and number of results.

TemplateService(String, String) - Constructor for class org.intermine.webservice.client.services.TemplateService

Use ServiceFactory instead of constructor for creating this service.

TemplateService.TemplateRequest - Class in org.intermine.webservice.client.services

A subclass of RequestImpl relevant to template queries.

TemplateService.TemplateRequest(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.services.TemplateService.TemplateRequest

Constructor.

TemplateSettingsForm - Class in org.intermine.web.struts

Form used when building a template.

TemplateSettingsForm() - Constructor for class org.intermine.web.struts.TemplateSettingsForm

TemplatesExecutionMap - Class in org.intermine.api.tracker

Class for saving the template executions into the memory.

TemplatesExecutionMap() - Constructor for class org.intermine.api.tracker.TemplatesExecutionMap

TemplatesExportAction - Class in org.intermine.web.struts

Exports templates to XML.

TemplatesExportAction() - Constructor for class org.intermine.web.struts.TemplatesExportAction

TemplatesImportAction - Class in org.intermine.web.struts

Imports templates in XML format.

TemplatesImportAction() - Constructor for class org.intermine.web.struts.TemplatesImportAction

TemplatesImportForm - Class in org.intermine.web.struts

Form bean representing template import form.

TemplatesImportForm() - Constructor for class org.intermine.web.struts.TemplatesImportForm

templateSummariser - Variable in class org.intermine.api.InterMineAPI

TemplateSummariser - Class in org.intermine.api.template

This class manages summaries of possible values for editable constraints for template queries.

TemplateSummariser(ObjectStore, ObjectStoreWriter, ObjectStoreSummary) - Constructor for class org.intermine.api.template.TemplateSummariser

Construct a TemplateSummariser.

TemplateToListService - Class in org.intermine.webservice.server.template

A service for turning the results of a template query into a list.

TemplateToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateToListService

Constructor

TemplateToListServlet - Class in org.intermine.webservice.server.template

Runs the template-to-list service to run templates and save them as lists.

TemplateToListServlet() - Constructor for class org.intermine.webservice.server.template.TemplateToListServlet

TemplateTrack - Class in org.intermine.api.tracker.track

Class to represent the track for the templates objects.

TemplateTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.TemplateTrack

Create a template track

TemplateTrack(String, String, String) - Constructor for class org.intermine.api.tracker.track.TemplateTrack

Create a template track

TEMPLATETRACK - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding

label for XML

TemplateTrackBinding - Class in org.intermine.api.tracker.xml

Code for reading and writing template tracks as XML.

TemplateTracker - Class in org.intermine.api.tracker

Class for tracking the templates execution by the users.

TemplateTracker(Queue<Track>) - Constructor for class org.intermine.api.tracker.TemplateTracker

TemplateTrackReadTask - Class in org.intermine.web.task

Task to read an templatetrack XML file of a webapp and saved into the userprofile database.

TemplateTrackReadTask() - Constructor for class org.intermine.web.task.TemplateTrackReadTask

TEMPLATETRACKS - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding

label for XML

TemplateTrackWriteTask - Class in org.intermine.web.task

Task to write an XML file of template track contained in the user profile database.

TemplateTrackWriteTask() - Constructor for class org.intermine.web.task.TemplateTrackWriteTask

TemplateUploadService - Class in org.intermine.webservice.server.template

A service to enable templates to be uploaded.

TemplateUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateUploadService

Constructor.

TemplateUploadServlet - Class in org.intermine.webservice.server.template

Runs the Template Upload Service to handle user template uploads.

TemplateUploadServlet() - Constructor for class org.intermine.webservice.server.template.TemplateUploadServlet

TemplateValue - Class in org.intermine.template

A TemplateValue represents the value for an editable constraint of a template query and details about what is being constrained.

TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue

Constructor.Construct with details of what we are constraining, but without the value.

TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue

Construct with the details of what we are constraining and the value.

TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, String, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue

Construct with the details of what we are constraining and the value.

TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, List<String>, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue

Construct with the details of what we are constraining and values.

TemplateValue.ValueType - Enum in org.intermine.template

Possible values for TemplateValue type.

TEN - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

TEN_THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

termClass - Variable in class org.intermine.bio.dataconversion.OboConverter

termClassName - Variable in class org.intermine.bio.dataconversion.GoConverter

termCollectionName - Variable in class org.intermine.bio.dataconversion.GoConverter

terms - Variable in class org.intermine.bio.ontology.OboParser

All terms.

TEST_STRING - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

TEXT_COUNT - Static variable in class org.intermine.webservice.client.core.ContentType

A ContentType constant that describes the generic text/plain content type when requesting counts.

TEXT_PLAIN - Static variable in class org.intermine.webservice.client.core.ContentType

A ContentType constant that describes the generic text/plain content type.

TEXT_TAB - Static variable in class org.intermine.webservice.client.core.ContentType

A ContentType constant that describes the generic text/plain content type.

TEXT_XML - Static variable in class org.intermine.webservice.client.core.ContentType

A ContentType constant that describes the generic text/xml content type.

TextUtil - Class in org.intermine.api.util

tgtDir - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask

tgtSequence - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler

then(Function<T, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor

Compose this visitor with a function which consumes the output of this visitor.

THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl

THREAD_COUNT - Static variable in class org.intermine.task.PrecomputeTask

throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer

Throws an exception.

throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose

Throws an exception.

tickle() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout

Tell this object to continue returning false from shouldCancelQuery.

tickleCount - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout

number of tickles. used to determine how.

time - Variable in class org.intermine.dataconversion.FullXmlConverter

timeLimit - Variable in class org.intermine.sql.precompute.BestQueryExplainer

times - Variable in class org.intermine.dataconversion.FullXmlConverter

timeSpentExecute - Variable in class org.intermine.dataloader.BatchingFetcher

timeSpentPrefetchEquiv - Variable in class org.intermine.dataloader.BatchingFetcher

timeSpentPrefetchTracker - Variable in class org.intermine.dataloader.BatchingFetcher

timeSpentRecursing - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl

timestamp - Variable in class org.intermine.api.tracker.track.TrackAbstract

toArray() - Method in class org.intermine.util.PseudoSet

toArray(T[]) - Method in class org.intermine.util.PseudoSet

toArray() - Method in class org.intermine.webservice.client.results.ResultRowList

toArray(T[]) - Method in class org.intermine.webservice.client.results.ResultRowList

toBED() - Method in class org.intermine.bio.io.bed.BEDRecord

Return this record in BED format.

toBED() - Method in class org.intermine.bio.io.gaf.GAFRecord

Return this record in BED format.

toGFF3() - Method in class org.intermine.bio.io.gff3.GFF3Record

Return this record in GFF format.

toIntegers(Collection<String>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Convert a set of Strings to a set of Integers using identifierToId()

toItems(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer

Convert a collection of Objects to Item format.

toJson() - Method in class org.intermine.pathquery.PathQuery

Convert this PathQuery to a JSON serialisation.

toJson(boolean) - Method in class org.intermine.pathquery.PathQuery

Convert this PathQuery to a JSON serialisation.

toJSON() - Method in class org.intermine.template.TemplateQuery

Returns a JSON string representation of the template query.

toJSON(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter

Get the JSONObject that represents each cell in the results row

token - Variable in class org.intermine.web.struts.PasswordResetForm

tokenFactory - Variable in class org.intermine.webservice.server.user.NewDeletionTokenService

tokenHasMoreUses(String) - Method in class org.intermine.api.profile.ProfileManager

Return whether the token given in input is suitable for using in the future.

tokenise(String) - Method in class org.intermine.api.query.LookupTokeniser

Transform an input string into a list of identifiers.

TokenService - Class in org.intermine.webservice.server.user

A service that issues new tokens to a user.

TokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokenService

TokenServlet - Class in org.intermine.webservice.server.user

TokenServlet() - Constructor for class org.intermine.webservice.server.user.TokenServlet

TokensService - Class in org.intermine.webservice.server.user

Service that lets a user inspect their currently active tokens

TokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokensService

toMap() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref

toMap(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter

toProperties() - Method in class org.intermine.objectstore.ObjectStoreSummary

Convert this summary to a properties object

toQuery() - Method in class org.intermine.objectstore.query.iql.IqlQuery

Convert to a InterMine query

TorqueModelOutput - Class in org.intermine.objectstore.intermine

Map InterMine metadata to a Torque database schema in InterMine format

TorqueModelOutput(DatabaseSchema, File) - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutput

Constructor for this class

TorqueModelOutputTask - Class in org.intermine.objectstore.intermine

Creates and runs a ModelOutput process to generate java or config files.

TorqueModelOutputTask() - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutputTask

toString() - Method in class org.intermine.api.bag.BagQuery

toString() - Method in class org.intermine.api.bag.SharingInvite

toString() - Method in class org.intermine.api.beans.ObjectDetails

toString() - Method in class org.intermine.api.beans.PartnerLink

toString() - Method in class org.intermine.api.idresolution.ResolutionJob

toString() - Method in class org.intermine.api.mines.ObjectRequest

toString() - Method in class org.intermine.api.profile.BagValue

toString() - Method in class org.intermine.api.profile.InterMineBag

toString() - Method in class org.intermine.api.results.Column

toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue

toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue

toString() - Method in class org.intermine.api.results.ResultElement

Returns a String representation of the ResultElement.

toString() - Method in class org.intermine.api.search.SearchResult

toString() - Method in class org.intermine.api.search.SearchTarget

toString() - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder

toString() - Method in class org.intermine.bio.io.bed.BEDRecord

toString() - Method in class org.intermine.bio.io.gaf.GAFRecord

toString() - Method in class org.intermine.bio.io.gff3.GFF3Record

toString() - Method in class org.intermine.bio.ontology.OboTerm

Create a string representation of the term.

toString() - Method in class org.intermine.bio.ontology.OboTermSynonym

toString() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc

toString() - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Converts the Clob into a String.

toString() - Method in class org.intermine.bio.util.OrganismData

toString() - Method in class org.intermine.dataconversion.MockItemWriter

toString() - Method in class org.intermine.dataloader.Source

toString() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl

toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.BagTableToRemove

Returns the SQL statement that will drop the table.

toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

toString() - Method in class org.intermine.objectstore.proxy.ProxyCollection

We override this here in order to prevent possible infinite recursion.

toString() - Method in class org.intermine.objectstore.proxy.ProxyReference

toString() - Method in class org.intermine.objectstore.query.ClobAccess

Converts the Clob into a String.

toString() - Method in class org.intermine.objectstore.query.ConstraintSet

toString() - Method in class org.intermine.objectstore.query.ContainsConstraint

toString() - Method in class org.intermine.objectstore.query.iql.IqlQuery

Return a string version of the IqlQuery

toString() - Method in class org.intermine.objectstore.query.OverlapConstraint

toString() - Method in class org.intermine.objectstore.query.OverlapRange

toString() - Method in class org.intermine.objectstore.query.PendingClob

Converts the Clob into a String.

toString() - Method in class org.intermine.objectstore.query.Query

Returns a string representation of this Query object

toString() - Method in class org.intermine.objectstore.query.QueryClass

Returns a String representation.

toString() - Method in class org.intermine.objectstore.query.QueryClassBag

Returns a String representation.

toString() - Method in class org.intermine.objectstore.query.QueryField

Produces a String, for debugging purposes.

toString() - Method in class org.intermine.objectstore.query.QueryObjectReference

toString() - Method in class org.intermine.objectstore.query.QueryValue

toString() - Method in class org.intermine.objectstore.query.Results

toString() - Method in class org.intermine.objectstore.query.ResultsInfo

toString() - Method in class org.intermine.objectstore.query.SimpleConstraint

toString() - Method in class org.intermine.objectstore.query.UnknownTypeValue

toString() - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl

toString() - Method in class org.intermine.pathquery.LogicExpression.Operator

Produce an expression for this branch of the tree.

toString() - Method in class org.intermine.pathquery.LogicExpression

Get the expression as a string.

toString() - Method in class org.intermine.pathquery.LogicExpression.Variable

Just returns the variable name.

toString() - Method in class org.intermine.pathquery.Node

toString() - Method in class org.intermine.pathquery.OrderElement

toString() - Method in class org.intermine.pathquery.Path

Returns a representation of the Path as a String, with class constraint markers.

toString() - Method in class org.intermine.pathquery.PathConstraintAttribute

toString() - Method in class org.intermine.pathquery.PathConstraintBag

toString() - Method in class org.intermine.pathquery.PathConstraintIds

toString() - Method in class org.intermine.pathquery.PathConstraintLookup

toString() - Method in class org.intermine.pathquery.PathConstraintLoop

toString() - Method in class org.intermine.pathquery.PathConstraintMultiValue

toString() - Method in class org.intermine.pathquery.PathConstraintNull

toString() - Method in class org.intermine.pathquery.PathConstraintSubclass

toString() - Method in class org.intermine.pathquery.PathQuery

Converts this object into a rudimentary String format, containing all the data.

toString() - Method in class org.intermine.sql.Database

toString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate

toString() - Method in class org.intermine.sql.precompute.PrecomputedTable

toString() - Method in class org.intermine.sql.query.Constant

toString() - Method in class org.intermine.sql.query.Constraint

toString() - Method in class org.intermine.sql.query.ExplainResult

toString() - Method in class org.intermine.sql.query.OrderDescending

toString() - Method in class org.intermine.sql.query.Query

Overrides Object.toString().

toString() - Method in class org.intermine.sql.query.Table

A toString method, which helps us when debugging.

toString() - Method in class org.intermine.template.TemplateQuery

toString() - Method in class org.intermine.template.TemplateValue

toString() - Method in class org.intermine.util.AlwaysSet

toString() - Method in class org.intermine.util.IntPresentSet

toString() - Method in class org.intermine.util.IntToIntMap

toString() - Method in class org.intermine.util.ReferenceMap

toString() - Method in class org.intermine.web.logic.config.Displayer

Return an XML String of this Type object

toString(String) - Method in class org.intermine.web.logic.config.Displayer

Return an XML String of this Type object

toString() - Method in class org.intermine.web.logic.config.FieldConfig

toString() - Method in class org.intermine.web.logic.config.TableExportConfig

toString() - Method in class org.intermine.web.logic.config.Type

Return an XML String of this Type object

toString() - Method in class org.intermine.web.logic.config.WebConfig

Return an XML String of this WebConfig object

toString() - Method in class org.intermine.web.logic.query.MetadataNode

toString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath

Returns a representation of the Path as a String, with class constraint markers.

toString() - Method in class org.intermine.web.logic.results.InlineList

toString() - Method in class org.intermine.web.logic.template.ConstraintInput

toString() - Method in class org.intermine.web.logic.TreeNode

toString() - Method in class org.intermine.web.logic.WebUtil.HeadResource

toString() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig

Return an XML String of this Type object

toString() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig

Return an XML String of this Type object

toString() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity

toString() - Method in class org.intermine.web.struts.oauth2.MigrationMapping

toString() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement

toString() - Method in class org.intermine.web.tags.table.NavigationBarTag

toString() - Method in class org.intermine.webservice.client.core.ContentType

toString() - Method in class org.intermine.webservice.client.core.RequestImpl

toString() - Method in class org.intermine.webservice.client.core.Version

Returns string representation of Version that is send with request.

toString() - Method in class org.intermine.webservice.client.lists.ItemList

toString() - Method in class org.intermine.webservice.client.results.Item

toString() - Method in class org.intermine.webservice.server.core.Either.Left

toString() - Method in class org.intermine.webservice.server.core.Either.Right

toString() - Method in class org.intermine.webservice.server.core.Pair

toString() - Method in class org.intermine.webservice.server.core.SubTable

toString() - Method in class org.intermine.webservice.server.core.TableCell

toString() - Method in enum org.intermine.webservice.server.Format

toString() - Method in class org.intermine.webservice.server.JWTBuilder

toString() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput

toString() - Method in class org.intermine.xml.full.Item

toStringNoConstraints() - Method in class org.intermine.pathquery.Path

Returns a representation of the Path as a String, with no class constraint markers.

toStrings(Collection<Integer>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Convert a set of Integers to a set of String using idToIdentifier()

toStrings(List<Object>) - Method in class org.intermine.pathquery.PathQueryHandler

Convert a List of Objects to a List of Strings using toString

toStringTruncateParameters(int) - Method in class org.intermine.objectstore.query.iql.IqlQuery

Return a string version of the IqlQuery but truncated the parameters (lists of bag contents) to the specified length.

toXml() - Method in class org.intermine.pathquery.PathQuery

Convert a PathQuery to XML, using the default value of PathQuery.USERPROFILE_VERSION

toXml(int) - Method in class org.intermine.pathquery.PathQuery

Convert a PathQuery to XML.

toXml(int) - Method in class org.intermine.template.TemplateQuery

Convert a template query to XML.

TRAC_TICKET_URL_PREFIX - Static variable in class org.intermine.task.AcceptanceTestTask

Prefix of the ticket pages in Trac.

Track - Interface in org.intermine.api.tracker.track

Class representing the track

TrackAbstract - Class in org.intermine.api.tracker.track

long Class representing the track

TrackAbstract() - Constructor for class org.intermine.api.tracker.track.TrackAbstract

TrackAjaxServices - Class in org.intermine.dwr

TrackAjaxServices() - Constructor for class org.intermine.dwr.TrackAjaxServices

Construct a ajax services object that does tracking stuff.

Tracker - Interface in org.intermine.api.tracker

Interface to represent a Tracker, an object tracking the users activities in the webapp into the database

trackerDelegate - Variable in class org.intermine.api.InterMineAPI

TrackerDelegate - Class in org.intermine.api.tracker

Intermediate class which decouples the tracker components from the code that uses them.

TrackerDelegate(String[], ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.TrackerDelegate

Create the tracker manager managing the trackers specified in input

TrackerFactory - Class in org.intermine.api.tracker.factory

Factory to instantiate the trackers with the reflection

trackerLogger - Variable in class org.intermine.api.tracker.AbstractTracker

TrackerLogger - Class in org.intermine.api.tracker

Runnable object providing insertion into the database.

TrackerLogger(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.TrackerLogger

Construct a TrackerLogger for a specific connection and table

trackerLoggerThread - Variable in class org.intermine.api.tracker.TrackerDelegate

trackerMissingClasses - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

trackers - Variable in class org.intermine.api.tracker.TrackerDelegate

TrackerUtil - Class in org.intermine.api.tracker.util

TrackHandler - Class in org.intermine.api.tracker.xml

TrackHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackHandler

trackKeywordSearch(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the login event

trackList(String, int, ListBuildMode, ListTrackerEvent, Profile, String) - Method in class org.intermine.api.tracker.ListTracker

trackListCreation(String, int, ListBuildMode, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the list creation

trackListExecution(String, int, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the list execution

trackLogin(String) - Method in class org.intermine.api.tracker.LoginTracker

Track when the user logs in his account

trackLogin(String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the login event

TrackManagerBinding - Class in org.intermine.api.tracker.xml

Code for reading and writing all tracks objects as XML

TrackManagerHandler - Class in org.intermine.api.tracker.xml

Event handler for the track xml file

TrackManagerHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackManagerHandler

Create a new TrackHandler

trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.QueryTracker

trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the execution of a query (saved or temporary)

trackQueue - Variable in class org.intermine.api.tracker.AbstractTracker

trackSearch(String, Profile, String) - Method in class org.intermine.api.tracker.KeySearchTracker

Record the search.

trackTableName - Variable in class org.intermine.api.tracker.AbstractTracker

trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TemplateTracker

Store into the database the template execution by the user or if the user is not logged during a specific http session.

trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Store into the database the template execution by the user specified in input

TransferInterruptedException - Exception in org.intermine.webservice.client.exceptions

TransferInterruptedException is the error thrown when a service returns an incomplete result set.

TransferInterruptedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException

TransferInterruptedException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException

TransferInterruptedException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException

TransferInterruptedException() - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException

Construct a new TransferInterrupted Exception.

TransferSequences - Class in org.intermine.bio.postprocess

Transfer sequences from the Assembly objects to the other objects that are located on the Assemblys and to the objects that the Assemblys are located on (eg.

TransferSequences(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.TransferSequences

Create a new TransferSequences object from the given ObjectStoreWriter

transferToLocatedSequenceFeatures() - Method in class org.intermine.bio.postprocess.TransferSequences

Use the Location relations to copy the sequence from the Chromosomes to every SequenceFeature that is located on a Chromosome and which doesn't already have a sequence (ie. don't copy to Assembly).

transferToTranscripts() - Method in class org.intermine.bio.postprocess.TransferSequences

For each Transcript, join and transfer the sequences from the child Exons to a new Sequence object for the Transcript.

transform(Object) - Method in class org.intermine.api.profile.TagMapper

transform(Tag) - Method in class org.intermine.api.profile.TagMapper

Transform a tag into a string of some kind.

translate(char) - Method in class org.intermine.bio.util.ClobAccessReverseComplement

Translates a single character to the complement base for DNA.

translateFromDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Translate an object exiting the ObjectStore.

translateFromDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator

Translate an object exiting the ObjectStore.

translateIdToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Translate an object id into a native identifier.

translateIdToIdentifier(Integer) - Method in class org.intermine.objectstore.translating.Translator

Translate an object id into a native identifier.

translateQuery(Query) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Translate a query.

translateQuery(Query) - Method in class org.intermine.objectstore.translating.Translator

Translate a query.

translateToDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator

Translate an object entering the ObjectStore.

translateToDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator

Translate an object entering the ObjectStore.

Translator - Class in org.intermine.objectstore.translating

Interface specifying operations required for inline translation of queries and data objects by a translating ObjectStore.

Translator() - Constructor for class org.intermine.objectstore.translating.Translator

traverseConstraint(Constraint, Map<QueryEvaluable, ConstraintSet>) - Method in class org.intermine.api.bag.BagQuery

Finds all BagConstraints in a Constraint, and places the QueryEvaluable and the containing ConstraintSet into the given Map.

traverseConstraints(Constraint, ConstraintTraverseAction) - Static method in class org.intermine.objectstore.query.ConstraintHelper

Traverse the given Constraint tree (ie. recursively look for nested constraints if the argument is a ConstraintSet) and call ConstraintTraverseAction for each Constraint.

TreatStringTag - Class in org.intermine.web.tags.util

Tag escaping apostrophes, quotes and replacing "\n" with html tag for end of line.

TreatStringTag() - Constructor for class org.intermine.web.tags.util.TreatStringTag

TreeAction - Class in org.intermine.web.struts

Implementation of Action that modifies a tree.

TreeAction() - Constructor for class org.intermine.web.struts.TreeAction

TreeController - Class in org.intermine.web.struts

Perform initialisation steps for displaying a tree

TreeController() - Constructor for class org.intermine.web.struts.TreeController

TreeNode - Class in org.intermine.web.logic

Bean to represent one row in the display of a tree

TreeNode(Object, String, int, boolean, boolean, boolean, List<String>) - Constructor for class org.intermine.web.logic.TreeNode

Constructor

TreeWalker<L> - Class in org.intermine.webservice.server.core

A type alias to reduce type stuttering.

TreeWalker() - Constructor for class org.intermine.webservice.server.core.TreeWalker

TriageBagAction - Class in org.intermine.web.struts

An action to handle reparative actions to bags.

TriageBagAction() - Constructor for class org.intermine.web.struts.TriageBagAction

TriageBagForm - Class in org.intermine.web.struts

TriageBagForm() - Constructor for class org.intermine.web.struts.TriageBagForm

TRUE - Static variable in class org.intermine.objectstore.query.QueryValue

The true value

TRUNCATED_CLASSES - Static variable in class org.intermine.modelproduction.MetadataManager

The name of the key used to store the truncated classes string.

TSVFileReaderTask - Class in org.intermine.task

Read a file of tab separated values.

TSVFileReaderTask() - Constructor for class org.intermine.task.TSVFileReaderTask

type - Variable in class org.intermine.api.results.Column

type - Variable in class org.intermine.bio.dataconversion.UniprotEntry.Comment

type - Variable in class org.intermine.objectstore.query.QueryReference

type(String, String) - Static method in class org.intermine.pathquery.Constraints

Creates a constraint for a path to be a particular subclass (type).

type - Variable in class org.intermine.task.ModelOutputTask

Type - Class in org.intermine.web.logic.config

Configuration object for displaying a class

Type() - Constructor for class org.intermine.web.logic.config.Type

TYPE_BOOLEAN - Static variable in class org.intermine.objectstore.query.UnknownTypeValue

A value that indicates that the value represents a Boolean.

TYPE_CONVERTED - Static variable in class org.intermine.api.bag.BagQueryResult

Key of the Map returned by getIssues() when the object found when querying using input string needed to be translated.

TYPE_NUMBER - Static variable in class org.intermine.objectstore.query.UnknownTypeValue

A value that indicates that the value represents a number.

TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput

The type of the list

TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListsRequestParser

Name of parameter with object type.

TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService

Name of type parameter

TYPE_STRING - Static variable in class org.intermine.objectstore.query.UnknownTypeValue

A value that indicates that the value represents a String or Date.

TYPECAST - Static variable in class org.intermine.sql.query.Function

Type casts - takes two operands.

typeConstraintToJson(PathConstraint) - Method in class org.intermine.pathquery.PathQuery

format a type constraint to a JSON representation.

TypeConverter - Class in org.intermine.api.bag

Static helper routines to convert bags between different types.

types - Variable in class org.intermine.bio.ontology.OboParser

All relation types

types - Variable in class org.intermine.sql.precompute.PrecomputedTableManager

TYPES - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle

The parts that make up a header (main title, sub title)

U

unaccept() - Method in class org.intermine.api.bag.SharingInvite

UnauthorizedException - Exception in org.intermine.webservice.server.exceptions

UnauthorizedException() - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException

Construct an UnauthorizedException

UnauthorizedException(String) - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException

unescape(String) - Method in class org.intermine.bio.ontology.OboParser

Perform OBO unescaping.

unescape(String) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser

Unescapes a String, by removing quotes from the beginning and end.

UnhandledFeatureException - Exception in org.intermine.api.query.codegen

Exception representing the failure to encode a feature in the target language.

UnhandledFeatureException() - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException

Create an exception with a default message.

UnhandledFeatureException(String) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException

Create an exception with a given message.

UnhandledFeatureException(Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException

Create an exception when there is something to blame.

UnhandledFeatureException(String, Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException

Create an exception when there is a message and a cause

UNION - Static variable in class org.intermine.api.bag.BagOperations

Constant representing logical union.

union(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations

Create a bag that is the UNION of all the bags provided, if the union is the empty set then don't create the new bag - if bags are of incompatible types or are all empty.

Union - Class in org.intermine.api.bag.operations

Union(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Union

UNION - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination

Constant representing a UNION operation

UniprotConfig - Class in org.intermine.bio.dataconversion

UniprotConfig() - Constructor for class org.intermine.bio.dataconversion.UniprotConfig

read configuration file

UniprotConfig.ConfigEntry - Class in org.intermine.bio.dataconversion

class representing an organism in the uniprot config file

UniprotConfig.ConfigEntry() - Constructor for class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry

UniprotConfig.IdentifierConfig - Class in org.intermine.bio.dataconversion

class representing a line in the uniprot config file

UniprotConfig.IdentifierConfig(String, String) - Constructor for class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig

UniprotConverter - Class in org.intermine.bio.dataconversion

DataConverter to parse UniProt data into items.

UniprotConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.UniprotConverter

Constructor

UniprotConverter.DiseaseHolder - Class in org.intermine.bio.dataconversion

temporarily hold disease item until stored

UniprotConverter.DiseaseHolder() - Constructor for class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder

Constructor

UniprotEntry - Class in org.intermine.bio.dataconversion

holder class representing an entry in uniprot xml

UniprotEntry() - Constructor for class org.intermine.bio.dataconversion.UniprotEntry

constructor used for non-isoform entries

UniprotEntry(String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry

UniprotEntry.Comment - Class in org.intermine.bio.dataconversion

Class representing a comment in a uniprot entry.

UniprotEntry.Comment(String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry.Comment

UniprotEntry.Dbref - Class in org.intermine.bio.dataconversion

class representing a dbref entry in a uniprot entry

UniprotEntry.Dbref(String, String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry.Dbref

UniProtFastaLoaderTask - Class in org.intermine.bio.dataconversion

Code for loading fasta for uniprot proteins.

UniProtFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.UniProtFastaLoaderTask

UniprotFilterTask - Class in org.intermine.bio.dataconversion

Read a set of Uniprot XML files and write out only those elements for an organism in the given set of names.

UniprotFilterTask() - Constructor for class org.intermine.bio.dataconversion.UniprotFilterTask

UniprotKeywordConverter - Class in org.intermine.bio.dataconversion

Importer to add descriptions to UniProt keywords

UniprotKeywordConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.UniprotKeywordConverter

Constructor

UniprotXmlFilter - Class in org.intermine.bio.dataconversion

Extract only entries for organisms of interest from UniProt XML dump files.

UniprotXmlFilter(Set) - Constructor for class org.intermine.bio.dataconversion.UniprotXmlFilter

Construct a filter with a set of organism full names to extract entries for.

UNIQUE_INTEGER_SEQUENCE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

The name of the SEQUENCE in the database to use when generating unique integers in getUniqueInteger().

UNIQUE_KEYS - Static variable in class org.intermine.api.profile.UserPreferences

Common keys

uniqueColumnValues(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor

Get the the total number of unique column values for a given path in the context of a given query.

uniqueId - Variable in class org.intermine.bio.dataconversion.OboConverter

uniqueSynId - Variable in class org.intermine.bio.dataconversion.OboConverter

UNIX_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter

Unix line separator only LF

UnknownBagTypeException - Exception in org.intermine.api.bag

Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.

UnknownBagTypeException(String) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException

Constructs an IncompatibleBagTypesException with the specified detail message.

UnknownBagTypeException(Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException

Constructs an IncompatibleBagTypesException with the specified nested throwable.

UnknownBagTypeException(String, Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException

Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.

UnknownTypeValue - Class in org.intermine.objectstore.query

Represents a value with an unknown type.

UnknownTypeValue(String) - Constructor for class org.intermine.objectstore.query.UnknownTypeValue

Constructor.

unmarhsal(InputStream) - Static method in class org.intermine.web.logic.aspects.AspectBinding

Read data set configuration from an input stream.

unmarshal(Reader, ObjectStoreWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding

Read the template tracks from an XML stream Reader.

unmarshal(Reader, ObjectStoreWriter, ObjectStoreWriter, Integer) - Static method in class org.intermine.api.xml.InterMineBagBinding

Parse saved queries from a Reader

unmarshal(Reader, ProfileManager, String, String, Set<Tag>, ObjectStoreWriter, int) - Static method in class org.intermine.api.xml.ProfileBinding

Read a Profile from an XML stream Reader.

unmarshal(Reader, ProfileManager, ObjectStoreWriter, boolean) - Static method in class org.intermine.api.xml.ProfileManagerBinding

Read a ProfileManager from an XML stream Reader

unmarshal(Reader, ProfileManager, ObjectStoreWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding

Read a ProfileManager from an XML stream Reader.

unmarshal(Reader, Map, int) - Static method in class org.intermine.api.xml.SavedQueryBinding

Parse TemplateQuerys from XML

unmarshal(Reader, Integer) - Static method in class org.intermine.api.xml.SharedBagBinding

Parse saved queries from a Reader.

unmarshal(ProfileManager, String, Reader) - Method in class org.intermine.api.xml.TagBinding

Parse Tags from XML and write them to the userprofile object store

unmarshal(InputStream) - Method in class org.intermine.util.XmlBinding

Unmarshal an XML file to an object.

unmarshal(Reader) - Static method in class org.intermine.web.logic.aspects.AspectBinding

Read in data set configuration from XML.

unmarshalPathQueries(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding

Parse PathQueries from XML.

unmarshalPathQueries(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding

Parse PathQueries from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.

unmarshalPathQuery(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding

Parses PathQuery from XML.

unmarshalPathQuery(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding

Parses a PathQuery from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.

unmarshalTemplates(Reader, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding

Parse TemplateQueries from XML.

unshareAllBagsFromUser(Profile, Profile) - Method in class org.intermine.api.bag.SharedBagManager

Stop sharing all bags owned by the given user which have been shared with the given recipient.

unshareBagWithAllUsers(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager

Delete the sharing between the bag and all the users sharing the bag.

unshareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager

Unshare the bag with the user given in input

unshareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager

Un-share the bag with the user given in input

unshareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager

Delete the sharing between the user and the bag given in input

unverbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

Deprecated.

ajaxVerbosify is used instead

uosw - Variable in class org.intermine.api.bag.SharedBagManager

uosw - Variable in class org.intermine.api.profile.ProfileManager

upcast(Map<String, TemplateQuery>) - Static method in class org.intermine.api.template.TemplateHelper

Transform a map of templates into a map of API templates.

update() - Method in class org.intermine.api.profile.ModelUpdate

Update bags, savedquery and savedtemplatequery if class has been renamed -> update type bags, update savedquery and savedtemplatequery if a field has been renamed -> update savedquery and savedtemplatequery if class has been deleted -> delete bags with that type

update(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate

Update the path query

updateBagType(String, String) - Method in class org.intermine.api.profile.Profile

Update the type of bag.

updateColumnValue(Database, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil

Set the default value in a column for all values where the current value is null.

updateColumnValue(Connection, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil

Set the default value in a column for all values.

updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate

Update the constraint with the renamed classes or/and fields

updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.TemplateQueryUpdate

UpdateListTablesTask - Class in org.intermine.web.task

Task that rename the column 'intermine_current' into 'intermine_state' in savedbag table (from boolean to text) and add the column 'extra' (and its value) in the bagvalues table

UpdateListTablesTask() - Constructor for class org.intermine.web.task.UpdateListTablesTask

updatePopulationQuery(Query, Query, QueryField) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Update the annotated population query given in input using the queryfield specific for the correction

updateQueryWithCorrectionCoefficient(Query, QueryClass) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient

Update the query, given in input, with the field associated with the correction coefficient and return a query field.

updateReferredQueryAndTemplate() - Method in class org.intermine.api.profile.ModelUpdate

Update savedquery and savedtemplatequery when they reeferring to renamed classes or fields

updateStatistics(Map<String, Integer>, Connection) - Method in interface org.intermine.sql.writebatch.BatchWriter

Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.

updateStatistics(Map<String, Integer>, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.

updateTags() - Method in class org.intermine.webservice.client.lists.ItemList

Make sure that the tags on this object are up-to-date with those stored on the server.

updateTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile

Update an existing template, throw exceptions when template doesn't exist.

updateTemplate(String, String) - Method in class org.intermine.dwr.AjaxServices

Update with the value given in input the field of the previous template saved into the session

updateTemplateName(String, String, Connection) - Method in class org.intermine.api.tracker.TemplateTracker

Update the template name value into the database

updateTemplateName(String, String) - Method in class org.intermine.api.tracker.TrackerDelegate

Update the template name value into the database

UpdateTrackTableTask - Class in org.intermine.web.task

Task to modify the type of the column 'timestamp' in the templatetrack table in the userprofile database.

UpdateTrackTableTask() - Constructor for class org.intermine.web.task.UpdateTrackTableTask

updateTypeBag() - Method in class org.intermine.api.profile.ModelUpdate

Update the type to all bags having as a type one of the classes renamed

updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.profile.Profile

Update the user repository with the sharedbags

updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.search.UserRepository

Update the user repository with the shared bags

UpgradeBagList - Class in org.intermine.web.logic.profile

Runnable object providing upgrading osbag_int table.

UpgradeBagList(Profile, BagQueryRunner) - Constructor for class org.intermine.web.logic.profile.UpgradeBagList

Constructor

UpgradeJob - Class in org.intermine.api.idresolution

UpgradeJob(UUID, BagQueryUpgrade) - Constructor for class org.intermine.api.idresolution.UpgradeJob

upgradeOsb(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag

Upgrades the ObjectStoreBag with a new ObjectStoreBag containing the collection of elements given in input

UPGRADING_BAG - Static variable in class org.intermine.web.logic.Constants

Key for the upgrading bag on the session

UPPER - Static variable in class org.intermine.objectstore.query.QueryExpression

Upper case version of the given string

UPPER - Static variable in class org.intermine.sql.query.Function

UPPER operator - takes one operand

URLGenerator - Class in org.intermine.web.util

Class generating useful links like base link: http://localhost:8080/query

URLGenerator(HttpServletRequest) - Constructor for class org.intermine.web.util.URLGenerator

Constructor.

URLParser - Class in org.intermine.webservice.client.util

The URLParse class is util class for parsing URL.

URLUtil - Class in org.intermine.web.util

Util class for URL processing.

USAGE - Static variable in class org.intermine.webservice.server.lists.ListDeletionService

Usage information to help users who provide incorrect input.

USAGE - Static variable in class org.intermine.webservice.server.lists.ListRenameService

Usage information to help users who provide incorrect input.

USAGE - Static variable in class org.intermine.webservice.server.lists.ListUploadService

A usage string to return for bad requests.

useJoin - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm

USER - Static variable in class org.intermine.api.search.Scope

User scope for private bags, templates, etc.

user - Variable in class org.intermine.task.GrantTask

USER_BAGS - Static variable in class org.intermine.api.search.SearchTarget

The search target for user bags

USER_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget

The search target for user templates

UserAlreadyShareBagException - Exception in org.intermine.api.profile

Exception thrown when a user already shares the bag.

UserAlreadyShareBagException() - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException

Constructor

UserAlreadyShareBagException(String) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException

Constructor with message.

UserAlreadyShareBagException(Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException

Constructor with throwable

UserAlreadyShareBagException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException

Constructor with message and throwable

UserAlreadyShareBagException(SavedBag, UserProfile) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException

Constructor with the actual objects we are trying to link.

useRangeTypes - Variable in class org.intermine.objectstore.intermine.DatabaseSchema

useRangeTypes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema

Returns true if we can use Postgres built-in range types on this database.

UserDataFormatter - Class in org.intermine.webservice.server.user

A class that processes information about a user into XML.

UserDataFormatter() - Constructor for class org.intermine.webservice.server.user.UserDataFormatter

userId - Variable in class org.intermine.api.profile.Profile

username - Variable in class org.intermine.api.profile.Profile

userName - Variable in class org.intermine.api.tracker.track.TrackAbstract

USERNAME - Static variable in class org.intermine.api.util.AnonProfile

The user name of the anonymous user.

USERNAME - Static variable in class org.intermine.web.logic.Constants

The display name of the current user

username - Variable in class org.intermine.web.struts.CreateAccountForm

username - Variable in class org.intermine.web.struts.LoginForm

username - Variable in class org.intermine.web.struts.RequestPasswordForm

username - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

UserNotFoundException - Exception in org.intermine.api.profile

Exception thrown when user is not found.

UserNotFoundException(String) - Constructor for exception org.intermine.api.profile.UserNotFoundException

Constructor with message.

UserNotFoundException(Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException

Constructor with throwable

UserNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException

Constructor with message and nested exception.

UserPreferences - Class in org.intermine.api.profile

UserPreferences(PreferencesManager, Profile) - Constructor for class org.intermine.api.profile.UserPreferences

USERPROFILE_VERSION - Static variable in class org.intermine.pathquery.PathQuery

Version number for the userprofile and PathQuery XML format.

userProfileAlias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

userProfileOS - Variable in class org.intermine.web.task.PrecomputeTemplatesTask

UserRepository - Class in org.intermine.api.search

A repository for searching the searchable items of a single user.

UserRepository(Profile) - Constructor for class org.intermine.api.search.UserRepository

Constructor.

UsersController - Class in org.intermine.web.struts

Controller for the users admin page

UsersController() - Constructor for class org.intermine.web.struts.UsersController

UserTemplateAction - Class in org.intermine.web.struts

Make some change to a user template.

UserTemplateAction() - Constructor for class org.intermine.web.struts.UserTemplateAction

V

v - Variable in class org.intermine.sql.query.SelectValue

VALID_OPS - Static variable in class org.intermine.objectstore.query.BagConstraint

List of possible operations

VALID_OPS - Static variable in class org.intermine.objectstore.query.ClassConstraint

Valid operators for this constraint.

VALID_OPS - Static variable in class org.intermine.objectstore.query.ConstraintSet

VALID_OPS - Static variable in class org.intermine.objectstore.query.ContainsConstraint

List of possible operations

VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryConstraint

VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryExistsConstraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintAttribute

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintBag

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintIds

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintLoop

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultitype

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultiValue

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintNull

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintRange

List of valid ops for this type of constraint

VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintSubclass

List of valid ops for this type of constraint

VALID_OPS_NULL - Static variable in class org.intermine.objectstore.query.ContainsConstraint

List of possible null operations

validate() - Method in class org.intermine.api.tracker.track.KeySearchTrack

validate() - Method in class org.intermine.api.tracker.track.ListTrack

Validate the track before saving into the database

validate() - Method in class org.intermine.api.tracker.track.LoginTrack

Validate the track before saving into the database

validate() - Method in class org.intermine.api.tracker.track.QueryTrack

validate() - Method in class org.intermine.api.tracker.track.TemplateTrack

Validate the track before saving into the database

validate() - Method in interface org.intermine.api.tracker.track.Track

Validate the track before saving into the database

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm

When there are no other errors, check email address is valid.

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportQueriesForm

Call inherited method then check whether xml is valid.

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm

validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplatesImportForm

Call inherited method then check whether xml is valid.

validate(String, String) - Method in class org.intermine.webservice.server.query.result.XMLValidator

Validates an XML string according to an XML Schema at a given URL.

validateBagName(String) - Static method in class org.intermine.dwr.AjaxServices

validate bag upload

validateBagOperations(String, String[], String) - Static method in class org.intermine.dwr.AjaxServices

validation that happens before new bag is saved

validateForGroups(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression

Validates an expression for the given groups of codes, making sure each group is only ANDed together.

validateLookupConstraints() - Method in class org.intermine.template.TemplateQuery

Verify templates don't contain non-editable lookup constraints

validateName(Collection<String>, String) - Static method in class org.intermine.api.util.NameUtil

Checks that the name doesn't already exist and returns a numbered name if it does.

validateName(String) - Method in class org.intermine.pathquery.PathQueryHandler

Checks that the query has a name and that there's no name duplicates and appends a number to the name if there is.

validatePath(String, Model) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil

Path should be of the form: Class1 ref1 Class2 ref2 Class3 Where the number of elements is greater than one and an odd number.

validateRequiredParams() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput

validateRequiredParams() - Method in class org.intermine.webservice.server.lists.CommutativeOperationInput

validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListInput

Check that the required parameters are there

validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListRenameInput

validateState() - Method in class org.intermine.webservice.server.core.ReadWriteJSONService

validateState() - Method in class org.intermine.webservice.server.lists.AuthenticatedListService

validateState() - Method in class org.intermine.webservice.server.lists.ListMakerService

validateState() - Method in class org.intermine.webservice.server.query.QueryToListService

validateState() - Method in class org.intermine.webservice.server.query.QueryUploadService

validateState() - Method in class org.intermine.webservice.server.template.TemplateRemovalService

validateState() - Method in class org.intermine.webservice.server.template.TemplateUploadService

validateState() - Method in class org.intermine.webservice.server.user.DeregistrationService

validateState() - Method in class org.intermine.webservice.server.user.NewUserService

validateState() - Method in class org.intermine.webservice.server.user.WhoAmIService

validateState() - Method in class org.intermine.webservice.server.WebService

Subclasses can put initialisation checks here.

validateWidgetsConfig(Model) - Method in class org.intermine.web.logic.config.WebConfig

Validate the content (the paths) in the widget config

validChromosomes() - Static method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory

Get a set of valid chromosome identifiers for human as we want to ignore other data types

validComparison(Class<?>, ConstraintOp, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint

Check whether a comparison is valid i.e. the arguments are comparable types and the the operator is permitted for those types

validOps - Variable in class org.intermine.objectstore.query.OverlapConstraint

validOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint

Return the list of valid (binary) operator codes given arguments of a specified type

validPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager

Validate a user's password A check should be made prior to this call to ensure a Profile exists

value - Variable in class org.intermine.sql.query.Constant

valueConstraintToJson(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery

Format a value constraint to a JSON representation.

valueEquals(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue

Compare the value of this AbstractValue with another to see if it is equal.

valueMap - Variable in class org.intermine.sql.precompute.PrecomputedTable

valueOf(String) - Static method in enum org.intermine.api.idresolution.Job.JobStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.lucene.KeywordSearchFacetType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.mines.ContentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.profile.BagState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.profile.TagMapper.Field

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.search.TaggingEvent.TagChange

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListBuildMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.pathquery.OrderDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.pathquery.OuterJoinStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.sql.DatabaseUtil.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.template.SwitchOffAbility

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.template.TemplateValue.ValueType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.MessageFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.ResponseType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.client.core.Request.RequestType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.Format

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.intermine.api.idresolution.Job.JobStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.lucene.KeywordSearchFacetType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.mines.ContentType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.profile.BagState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.profile.TagMapper.Field

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.search.TaggingEvent.TagChange

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.tracker.util.ListBuildMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.pathquery.OrderDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.pathquery.OuterJoinStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.sql.DatabaseUtil.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.template.SwitchOffAbility

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.template.TemplateValue.ValueType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class org.intermine.util.AlwaysMap

values() - Method in class org.intermine.util.IdentityMap

values() - Method in class org.intermine.util.ReferenceMap

values() - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.web.struts.oauth2.MessageFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.web.struts.oauth2.ResponseType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.client.core.Request.RequestType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.Format

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType

Returns an array containing the constants of this enum type, in the order they are declared.

VALUES_TEMPLATE - Static variable in class org.intermine.api.config.Constants

returns available queryable values for mine

verboseQueryLog - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

verbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails

Deprecated.

ajaxVerbosify is used instead

VERIFICATION_STRATEGY - Static variable in class org.intermine.webservice.server.JWTVerifier

The strategy used to verify tokens

verifiedSources - Static variable in class org.intermine.dataloader.DataLoaderHelper

verify(Model, String) - Static method in class org.intermine.dataloader.PriorityConfig

Verifies the priorities config given the list of data sources.

verify(String) - Method in class org.intermine.webservice.server.JWTVerifier

Verify this token and return a verification result.

VERIFYAUDIENCE - Static variable in class org.intermine.webservice.server.JWTVerifier

This is the key used to establish whether we should verify the audience.

verifyColumnType(Connection, String, String, int) - Static method in class org.intermine.sql.DatabaseUtil

verifyQuery() - Method in class org.intermine.pathquery.PathQuery

Verifies the contents of this query against the model, and for internal integrity.

VerifyTokenTask - Class in org.intermine.web.task

A task to check that a token can be verified.

VerifyTokenTask() - Constructor for class org.intermine.web.task.VerifyTokenTask

version - Variable in class org.intermine.pathquery.PathQueryHandler

version - Variable in class org.intermine.sql.Database

VERSION - Static variable in class org.intermine.webservice.client.core.Service

The version of this client library.

Version - Class in org.intermine.webservice.client.core

Simple class representing service version.

Version(int, int, int) - Constructor for class org.intermine.webservice.client.core.Version

Constructor.

VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService

The key for the version parameter

VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService

The key for the version parameter

VersionService - Class in org.intermine.webservice.server

Service for returning the version of this service.

VersionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.VersionService

Constructor

VersionServlet - Class in org.intermine.webservice.server

Returns version of the deployed InterMine application.

VersionServlet() - Constructor for class org.intermine.webservice.server.VersionServlet

visible - Variable in class org.intermine.api.results.Column

visitLeft(A) - Method in class org.intermine.webservice.server.core.EitherVisitor

Override this to access the left hand side.

visitLeft(L) - Method in class org.intermine.webservice.server.core.TreeWalker

visitRight(B) - Method in class org.intermine.webservice.server.core.EitherVisitor

Override this to access the right hand side.

visitRight(DisjointRecursiveList<L>) - Method in class org.intermine.webservice.server.core.TreeWalker

W

waitForCurrentJobs() - Method in class org.intermine.sql.Database

Blocks until all the current pending jobs are finished.

wantsColumnHeaders() - Method in class org.intermine.webservice.server.WebService

Returns true if the request wants column headers as well as result rows

warning(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

}

wasSuccessful() - Method in interface org.intermine.api.idresolution.Job

wasSuccessful() - Method in class org.intermine.api.idresolution.ResolutionJob

wasSuccessful() - Method in class org.intermine.api.idresolution.UpgradeJob

WeakReferenceHashMap<K,V> - Class in org.intermine.util

This is a Map implementation designed specifically for people intending to create a cache.

WeakReferenceHashMap(int, float) - Constructor for class org.intermine.util.WeakReferenceHashMap

Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the given load factor.

WeakReferenceHashMap(int) - Constructor for class org.intermine.util.WeakReferenceHashMap

Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the default load factor, which is 0.75.

WeakReferenceHashMap() - Constructor for class org.intermine.util.WeakReferenceHashMap

Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75).

WeakReferenceHashMap(String) - Constructor for class org.intermine.util.WeakReferenceHashMap

Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75), and a name.

WeakReferenceHashMap(Map<K, V>) - Constructor for class org.intermine.util.WeakReferenceHashMap

Constructs a new WeakReferenceHashMap with the same mappings as the specified Map.

WeakReferenceMap<K,V> - Class in org.intermine.util

This is a Map implementation designed specifically for people intending to create a cache.

WeakReferenceMap() - Constructor for class org.intermine.util.WeakReferenceMap

WEB_PROPERTIES - Static variable in class org.intermine.web.logic.Constants

ServletContext attribute used to store web.properties

WEB_SERVICE_VERSION - Static variable in class org.intermine.web.logic.Constants

Current version of the InterMine WebService.

WEB_STATE - Static variable in class org.intermine.web.logic.Constants

Session attribute used to store WebState object.

webConfig - Variable in class org.intermine.web.logic.bag.BagConverter

WebConfig - Class in org.intermine.web.logic.config

Configuration object for web site

WebConfig() - Constructor for class org.intermine.web.logic.config.WebConfig

WEBCONFIG - Static variable in class org.intermine.web.logic.Constants

ServletContext attribute used to store the WebConfig object for the Model.

webConfig - Variable in class org.intermine.web.logic.results.InlineResultsTable

WebJobInput - Class in org.intermine.web.logic.bag

WebJobInput(String, Collection<String>, BuildBagForm) - Constructor for class org.intermine.web.logic.bag.WebJobInput

Create a web-job.

webProperties - Variable in class org.intermine.api.LinkRedirectManager

webProperties - Variable in class org.intermine.webservice.server.WebService

The properties this mine was configured with

WebResults - Class in org.intermine.api.results

The web version of a Results object.

WebResults(InterMineAPI, PathQuery, Results, Map<String, QuerySelectable>, Map<String, BagQueryResult>) - Constructor for class org.intermine.api.results.WebResults

Create a new WebResults object.

WebResultsExecutor - Class in org.intermine.api.query

Executes a PathQuery and returns a WebResults object, to be used when multi-row style results are required.

WebResultsExecutor(InterMineAPI, Profile) - Constructor for class org.intermine.api.query.WebResultsExecutor

Constructor with necessary objects to generate an ObjectStore query from a PathQuery and execute it.

WebSearchable - Interface in org.intermine.api.search

An interface implemented by objects that we want to index with Lucene.

WebSearchableListController - Class in org.intermine.web.struts

Controller for webSearchableList.tile

WebSearchableListController() - Constructor for class org.intermine.web.struts.WebSearchableListController

WebSearchWatcher - Interface in org.intermine.api.search

The interface for describing objects that listen to WebSearchables for events.

WebService - Class in org.intermine.webservice.server

Base class for web services.

WebService(InterMineAPI) - Constructor for class org.intermine.webservice.server.WebService

Construct the web service with the InterMine API object that gives access to the core InterMine functionality.

WebserviceCodeGenAction - Class in org.intermine.web.struts

Action to handle the web service code generation.

WebserviceCodeGenAction() - Constructor for class org.intermine.web.struts.WebserviceCodeGenAction

WebserviceCodeGenerator - Interface in org.intermine.api.query.codegen

Interface for web service code generation.

WebserviceCodeGenInfo - Class in org.intermine.api.query.codegen

Class to represent the information used to generate web service source code.

WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo

Constructor.

WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile, String) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo

WebServiceConstants - Class in org.intermine.webservice.server

WebServiceInput - Class in org.intermine.webservice.server

Base class for input classes used with web services.

WebServiceInput() - Constructor for class org.intermine.webservice.server.WebServiceInput

WebserviceJavaCodeGenerator - Class in org.intermine.api.query.codegen

This Class generates Java source code of web service client for path query and template query.

WebserviceJavaCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator

WebserviceJavaScriptCodeGenerator - Class in org.intermine.api.query.codegen

A Class for generating JavaScript that would run a given query.

WebserviceJavaScriptCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator

WebservicePerlCodeGenerator - Class in org.intermine.api.query.codegen

This Class generates Perl source code of web service client for path query and template query.

WebservicePerlCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePerlCodeGenerator

WebservicePythonCodeGenerator - Class in org.intermine.api.query.codegen

Class for generating Python code to run a query, using the intermine python library.

WebservicePythonCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePythonCodeGenerator

WebServiceRequestParser - Class in org.intermine.webservice.server

Base request parser that is used by advanced web service parsers.

WebServiceRequestParser() - Constructor for class org.intermine.webservice.server.WebServiceRequestParser

WebserviceRubyCodeGenerator - Class in org.intermine.api.query.codegen

WebserviceRubyCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator

WebServiceServlet - Class in org.intermine.webservice.server.core

A servlet which can be easily configured to define how to route requests, using standard RESTful semantics.

WebServiceServlet() - Constructor for class org.intermine.webservice.server.core.WebServiceServlet

Constructor

WebServiceServlet.Method - Enum in org.intermine.webservice.server.core

WebState - Class in org.intermine.web.logic.results

This class saves things related to the state of web GUI.

WebState() - Constructor for class org.intermine.web.logic.results.WebState

WebTable - Interface in org.intermine.api.results

A List that can understand ResultElement objects.

WebUtil - Class in org.intermine.web.logic

Utility methods for the web package.

WebUtil.HeadResource - Class in org.intermine.web.logic

A bean encapsulating a resource (js or css).

welcome(String) - Method in class org.intermine.util.Emailer

Welcome a user to the system.

welcome(String, Properties) - Static method in class org.intermine.util.MailUtils

Send a welcoming email to an email address

welcome(String) - Method in class org.intermine.web.context.NullMailer

where - Variable in class org.intermine.sql.query.Query

whereHavingSafe(Object, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator

Returns an array containing two boolean values.

WHITELIST - Static variable in class org.intermine.webservice.server.JWTVerifier

This is where we get the list of aliases from if the strategy is WHITELIST

WhoAmIService - Class in org.intermine.webservice.server.user

Class for retrieving information about the currently authenticated user.

WhoAmIService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.WhoAmIService

Constructor

WhoAmIServlet - Class in org.intermine.webservice.server.user

WhoAmIServlet() - Constructor for class org.intermine.webservice.server.user.WhoAmIServlet

Widget - Class in org.intermine.web.logic.widget

A representation of a query using a list tool.

Widget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.Widget

The constructor

Widget - Class in org.intermine.webservice.client.widget

A representation of a list analysis widget, containing the metadata necessary to describe its usage and to choose how and whether to display its results.

Widget(String, String, String, String, String, Collection<String>, Collection<String>, String, String) - Constructor for class org.intermine.webservice.client.widget.Widget

Constructor.

WidgetConfig - Class in org.intermine.web.logic.widget.config

Class representing a Widget Configuration

WidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.WidgetConfig

WidgetConfigUtil - Class in org.intermine.web.logic.widget.config

Utilities for handling the widget configuration

WidgetForm - Class in org.intermine.web.struts

WidgetForm() - Constructor for class org.intermine.web.struts.WidgetForm

Constructor

WidgetHelper - Interface in org.intermine.web.logic.widget

An Interface for widget Utils

widgetId - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput

WidgetLdr - Class in org.intermine.web.logic.widget

The class that performs the actual queries for widgets.

WidgetLdr(InterMineBag, ObjectStore, String, WidgetConfig) - Constructor for class org.intermine.web.logic.widget.WidgetLdr

WidgetOptions - Interface in org.intermine.web.logic.widget

The type of options a widget would expect to receive.

WidgetProcessor - Interface in org.intermine.webservice.server.widget

WidgetProcessorImpl - Class in org.intermine.webservice.server.widget

A base class for Widget Processors

WidgetProcessorImpl() - Constructor for class org.intermine.webservice.server.widget.WidgetProcessorImpl

WidgetProcessorImpl.WidgetType - Enum in org.intermine.webservice.server.widget

Of widget types there are several:

WidgetResultProcessor - Interface in org.intermine.webservice.server.widget

Interfaces for classes that are able to process the results that widgets return.

WidgetService - Class in org.intermine.webservice.client.services

A class for managing widget operations.

WidgetService(String, String) - Constructor for class org.intermine.webservice.client.services.WidgetService

Use ServiceFactory instead of constructor for creating this service .

WidgetService - Class in org.intermine.webservice.server.widget

WidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.WidgetService

Construct the webservice controller.

WidgetsRequestParser - Class in org.intermine.webservice.server.widget

Request processor for WidgetsService that process request, validates it and returns parsed input as a parameter object.

WidgetsRequestParser() - Constructor for class org.intermine.webservice.server.widget.WidgetsRequestParser

ListsRequestProcessor constructor.

WidgetsServiceInput - Class in org.intermine.webservice.server.widget

WidgetsServiceInput is parameter object representing parameters for the WidgetsService web service.

WidgetsServiceInput() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput

WidgetsServiceInput.Builder - Class in org.intermine.webservice.server.widget

Class to build Inputs for the Widget Service.

WidgetsServiceInput.Builder() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder

WidgetsServlet - Class in org.intermine.webservice.server.widget

Servlet running WidgetsService.

WidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.WidgetsServlet

width - Variable in class org.intermine.sql.query.ExplainResult

WIDTH_BUCKET - Static variable in class org.intermine.objectstore.query.QueryFunction

Get the bucket this value would be assigned in an equal-depth histogram.

WidthBucketFunction - Class in org.intermine.objectstore.query

Representation of a call to the Postgresql WIDTH_BUCKET function.

WidthBucketFunction(QueryEvaluable, QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.WidthBucketFunction

Constructor.

WILDCARD - Static variable in class org.intermine.api.bag.BagQueryResult

Key of the Map returned by getIssues() when the object found by querying with a wildcard.

WINDOWS_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter

Windows line separator CR+LF

withinRange(int) - Method in class org.intermine.webservice.server.core.Page

WormBaseIdResolverFactory - Class in org.intermine.bio.dataconversion

Create an IdResolver for Worm genes by querying tables in a WormBase chado database.

WormBaseIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

constructor

WormBaseIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.WormBaseIdResolverFactory

Construct with SO term of the feature type to read from chado database.

WormBaseProcessor - Class in org.intermine.bio.dataconversion

A converter for chado that handles WormBase specific configuration.

WormBaseProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.WormBaseProcessor

Create a new WormBaseChadoDBConverter.

write(int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream

write(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream

write(char[], int, int) - Method in class org.intermine.sql.logging.DatabaseWriter

Write a portion of an array to the database

write(Connection, Map<String, ? extends Table>, Set<String>) - Method in interface org.intermine.sql.writebatch.BatchWriter

Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.

write(Connection, Map<String, ? extends Table>, Set<String>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl

Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.

write(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream

write(byte[], int, int) - Method in class org.intermine.util.SensibleByteArrayOutputStream

write(XMLStreamWriter, Profile, ObjectStore) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask

Write template-queries and tags elements.

write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.core.ResultProcessor

Writes results to output.

write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.output.JSONResultProcessor

writeCount(int, Output) - Method in class org.intermine.webservice.server.core.CountProcessor

Write the count to the output.

writeLargeUTF(String) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream

Writes the given String to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.

writeLargeUTF(StringConstructor) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream

Writes the given StringConstructor to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.

writeLargeUTF(Collection<String>) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream

Writes the given Collection of Strings to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.

writePendingClobs(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl

Writes the contents of any pending Clobs to the database, and replaces them in the objects with a real ClobAccess object.

writers - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl

writeToFile(File) - Method in class org.intermine.bio.dataconversion.IdResolver

Write IdResolver contents to a flat file

writtenObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl

This is a list of the objects in the destination database that we have written to as a non-skeleton.

X

xml - Variable in class org.intermine.web.struts.ImportXMLForm

xml(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction

Load a query from path query XML passed as a request parameter.

XmlBinding - Class in org.intermine.util

Represents an XML mapping - performs XML (un)marshalling of objects/Full Data XML

XmlBinding(Model) - Constructor for class org.intermine.util.XmlBinding

Constructor

XmlDataLoader - Class in org.intermine.dataloader

Provides a method for unmarshalling XML given source into java business objects then calls store on each.

XmlDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.XmlDataLoader

XmlDataLoaderTask - Class in org.intermine.dataloader

Uses an IntegrationWriter to load data from XML format

XmlDataLoaderTask() - Constructor for class org.intermine.dataloader.XmlDataLoaderTask

XMLFormatter - Class in org.intermine.webservice.server.output

Formats data to XML format.

XMLFormatter() - Constructor for class org.intermine.webservice.server.output.XMLFormatter

XmlHelper - Class in org.intermine.xml

Static methods to assist parsing and rendering of XML.

xmlRes - Variable in class org.intermine.dataloader.XmlDataLoaderTask

xmlRes - Variable in class org.intermine.task.FullXmlConverterTask

XMLTableResult - Class in org.intermine.webservice.client.results

A utility class for parsing tab separated values in the results.

XMLTableResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.XMLTableResult

Constructor.

XMLTableResult(String) - Constructor for class org.intermine.webservice.client.results.XMLTableResult

Constructor.

XMLTableResult(BufferedReader) - Constructor for class org.intermine.webservice.client.results.XMLTableResult

Constructor with a reader.

xmlToTemplateMap(String, Map<String, InterMineBag>, int) - Static method in class org.intermine.api.template.TemplateHelper

Parse templates in XML format and return a map from template name to TemplateQuery.

XmlUtil - Class in org.intermine.util

General-purpose methods for manipulating URIs and XML schema types

XMLValidator - Class in org.intermine.webservice.server.query.result

XMLValidator is class that validates xml string according an XML Schema at specified url.

XMLValidator() - Constructor for class org.intermine.webservice.server.query.result.XMLValidator

XMLValidatorErrorHandler - Class in org.intermine.webservice.server.query.result

XMLValidatorErrorHandler() - Constructor for class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler

XMLWidgetProcessor - Class in org.intermine.webservice.server.widget

A processor for handling requests for widget metadata.

xrefs - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord

xrefs - Variable in class org.intermine.bio.dataconversion.OboConverter

Y

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryCast

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in interface org.intermine.objectstore.query.QueryEvaluable

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryExpression

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryField

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryForeignKey

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryFunction

Allows a caller to suggest to this object that it holds a value of a certain type.

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryValue

Allows a caller to suggest to this object that it holds a value of a certain type.

Z

ZERO - Static variable in class org.intermine.web.logic.widget.ErrorCorrection

ZERO_PROFILE_VERSION - Static variable in class org.intermine.api.xml.ProfileManagerBinding

Default version of profile if it is not specified.

ZfinIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion

ID resolver for ZFIN genes.

ZfinIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory

Construct without SO term of the feature type.

ZfinIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory

Construct with SO term of the feature type.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z